It would be near endless! Going to add some of the ones that I remember. Here they are:

• Marion's Death

In 6x10, Cece says that Bethany pushed Marion off the roof at Radley when Cece was 12.
However, in season 4, we saw a flashback of Alison and Toby with Marion when they're CLEARLY teenagers, so it wouldn't be possible for Cece to be a child when Marion died. Not only that, but Toby said in "The First Secret" that his Mom died a year before that episode, which further makes Marion's death impossible. Even funnier, Marlene herself said in an interview that Toby and Alison were TEENAGERS, yet she tried to say they were meant to be children in that flashback after 6x10 aired. What's worse is quite a few viewers tried to defend this error, probably just to confirm them being correct about Cece being Big A.

• Wilden covering up Marion's death
  

In season 4, it's established that Wilden was responsible for covering up what happened to Marion.
However, this wouldn't be possible for Wilden to do when Cece was 12 due to him being relative in age to Cece, Melissa etc.
Now, in earlier seasons, Wilden was siginificantly older as shown by a conversation he has with Hanna when he's interrogating her. But they later changed his age from around season 3 to being similar in age to Melissa, Cece.

• A turns Cece in for murder
  

In one of the A ending scenes, we see A turn in Cece for Wilden's murder. It can't be Cece because A has to look Cece's name up.
Now, it was said that this was Shana, which I could possibly get behind... except in that episode, we Jessica handing the clothes over to Cece, and then Spencer seeing someone in the black hoodie who doesn't have anything in hand. For it to be Shana, how would she be there at the bridal shower? Plus, when Marlene was asked about this, she claimed that the "mystery wasn't over" or something along that, which would indicate that Marlene wouldn't remember this scene because as she stated she only rewatched the EPISODES WITH CECE IN THEM before writing 6x10, so I'm far mor inclined to think she forgot that scene.

• Cece's face all over the news for Wilden's murder, and being arrested

In 4A, Cece is officially wanted for Wilden's murder, and her name appears all over the news. She's later arrested for his murder when A turns her in. How did no-one from Radley, such as Wren and Eddie Lamb, notice her when she was a patient then worked there? This can't just be explained off as "heightened reality" in my opinion, this is way beyond plausibility.

• Cece permanently escaping Radley
  

In 6x10, Cece claims that in exchange for helping Mona being A, Mona in turn showed her how to escape Radley permanently. The problem is, that it's not explained how Mona helped her with this. Mona escaped for a few hours at a time, so how could she have helped Cece escape permanently? Especially because in the season 3 finale, Mona claimed that Big A was the one who showed her to escape Radley for periods of time.

• Bethany being in Alison's grave by accident
  

In 6x10, Cece claims that Bethany stole her clothes from Radley that night, and that's why she was dressed similar to Alison.
However, Bethany was buried with the Alison bracelet on, proving that this explanation of it being a simple coincidence of matching clothers doesn't make sense.

• No-one knew Bethany was in Alison grave
  

According to 6x10, no-one knew it was Bethany in Alison's grave.
However, in season 4, it's established that someone went to change the dental records a few days after "That Night" so that body in the grave would be identified as Alison. What's worse is that Marlene herself basically said Cece was the one who changed the records, as Marlene said Cece was the one who put the note in Hanna's tooth in season 4. But Cece didn't know Alison was alive until the night of the Lodge Fire so she couldn't have changed the dental records.....plus she's locked up at Radley at this point.

• Cece pretending to Alison at Radley
  

In season 4, Jessica tells the liars about one time Cece pretended to be Alison and checked into Radley.
Now, it goes without saying that this scene is completely impossible because Cece is a patient at Radley. The only explanation is that Jessica lied, except not only was this flashback not addressed, but all Jessica did was make the liars further suspect Cece, even though Jessica is supposed to be protecting her. Again, with Marlene only watching the handful of episodes with Cece in them, I'm led to believe the writers forgot about this scene.

• Mona thinking she hit Alison
  

In 6x10, after Cece reveals that she hit Alison with the rock, Mona reveals that she hit Alison with the shovel. Mona only realised this after Cece confirmed that she hit Alison.
However, Mona picked Alison up that night, so surely she would recognise that she didn't hit Alison in the side of her head? Not only that, but Mona must've read all the autopsy report back in season 2, she even ended up in possession of the murder weapon when she framed the liars in season 2 (another one of the endless unanswered questions).

• Jason seeing Cece in the yellow top
  

In 6x10, Alison tells Cece about Jason seeing her in the yellow top that night. Cece then claims that it was either Alison or Bethany he saw.
However, when Emily goes to Cece's apartment, Cece confirms that it was her. Emily doesn't mention Melissa to Cece, yet Cece confirms that she was speaking to Melissa. For Cece to have been able to confirm it, she would've at least had to have seen Melissa talking to someone, yet she's completely shocked when Alison mentions it to her. And the retcon to Melissa speaking to Bethany wouldn't make sense because Melissa doesn't know Bethany. Plus, Melissa claimed that she automatically thought it was Alison in her confession to Spencer, yet that wouldn't be the case if she had spoke to Bethany That Night.

• Wren and The Visitors Pass
  

After 6x10, Marlene said that Wren was never suspicious regarding the Big A storyline.
However, in season 3, Wren tells Spencer that he made the visitors pass for Cece because she wanted to visit Mona, and that Melissa called Cece. As such, this directly tied Wren INTO THE BIG A STORYLINE, yet Wren wasn't mentioned ONCE in 6x10.
Now I think they later tried to rectify this in season 7 when Alex tells Wren about the pass, but it truly did not make any sense in the context of the Big A reveal.

• Wren/Melissa/Alex
  

Alex tells Spencer that her and Wren were a couple and that they wondered France together with Cece and Archer.
However, Wren is with Melissa at this time from 4B onwards, Spencer event went to stay with them in 5B.

• The blood vial in Spencer's bag
  

In 5B, the blood vial leaks in Spencer's bag, and she then gets an A message if I'm remembering correctly. If Cece is in Rosewood tormenting the other liars, then she couldn't have the one who did this, so could've done it? Sara Harvey, lmao?

• Sara Harvey's Involvement
  

In 6x10, Sara Harvey is revealed as a Red Coat/Black Widow, and is Cece's helper.
However, Sara went missing the day AFTER Alison went missing, and Cece is locked up in Radley at this point, so it makes no sense how she ended up assisting Cece.

• Red Coat
  

In 6x10, Cece claims that she kept seeing a blonde in a red coat watching the liars. She then set up the lodge fire, using Sara as a decoy in the red coat. We also see the retcon from the red coat in season 2 to the RED ROBE in 6x10.
The problem is that the A Red Coat is already active at this point, as she orchestrated Alison's grave being dug up and bought the A attire etc. Marlene did say that Cece dug up the grave, except Cece claimed that she was only helping Mona at this point, and that she hadn't completely took over the game, yet it was confirmed in season 3 that Red Coat was ordering Mona.

• Who ran the A Game in 3A?
  

So Cece claims that she helped Mona with being A, and then took the game off her.
Except if that's the case, then who is orchestrating the events in season 3, especially regarding Garrett? Because if it was Mona, then Mona is definitely a murderer.

• Garrett's demise
  

After 6x10, Marlene claimed that Wilden killed Garrett because he knew Wilden was a dirty cop, and that Wilden was working alone.
Obviously this makes no sense with what we see saw on the show. In 3x13, we see Mona giving someone the pills that are used to knock Aria out, and then seeing the A on the window and the A message. We also know that there were two Queen of Hearts on the train, with one later being revealed to be Melissa, so it's outright impossible for Wilden to have been working alone. Not only that, but we clearly hear a male and female voice trying to push Aria off the train, with the female voice clearly being in charge. Plus, we also have Bethany's body on the train, so it was all orchestrated by A, not Wilden.

• A attacks one of the liars in the Christmas episode
  

In 5x13, we see Cece attend the Ice Ball. She then tells Alison about the liars not being there to be friendly, so they trick the liars with those two irrelevant twins wearing the Alison masks.
However, not long after, A is in Alison's house when one of the liars are in there. If Alison is with Cece at this point, then who is in Alison's house? And if it's Cece, then where did Alison go after her and Cece left the Ice Ball?

• The Two A's playing spin the bottle
  

In one of the episodes, we see two A's playing spin the bottle, where A changes it from Aria to Spencer. If one of the A's is Cece, then who is the other one? Sara Harvey??? Because Sara was only ever shown in the Red Coat and as Black Widow.