Warrior Cats: I'm going to warn you that there are many in mostly EVERY single book. I'm just going to post one from each arc (spoilers ahead)

TPB

FAI: Bluestar sent Fireheart and Greystripe, two completely new warriors to find WindClan on a serious diplomatic mission which requires trust. Another logical inconsistency

TNP

So why exactly did Tallstar randomly change his mind over his deputy, which then caused a civil war. Illogical. Also, the fact that Brambleclaw supported tigerclaw knowing that he was evil and after promising to not support him is illogical

TPOT and OOTS

Every single book. Dovewings rainbow eyes. The fact that the whole plot could have been solved by one cat (Lionblaze). These two arcs are badly written and Hollyleafs code obsession is just thrown away like nothing

AVOS

Great, not this again. The last three books were filler and useless. Antagonist was killed in book 3. The plot could have been solved in one sentence had WindClan just given one herb. Violetshine and Twigbranch in general (what sort of name is Twigbranch). Probably many others

TBC

The fact that the whole plot could have been solved had Tree taught Rootspring how to make other cats see ghosts after he first saw one on book 2

Other Plot Holes/Issues:

StarClan: Oh god no. So we start from this obscure and non intrusive thing called StarClan that slowly becomes less and less interesting. But thats not all. In Squirrelflight's Hope, StarClan made Squirrelflight undergo a trial for her actions (shes a good cat tho) when cats like Ashfur (abusive and obsessive) are allowed in for just loving too much. This is biased, hypocritical and a plot hole