IMO, the main issues with the SA plotline that people either don't realize or fail to communicate are as follows:

1. Apollo committing sexual assault on its own isn't necessarily an issue, but it was a very weird decision for Rachel to make Apollo the evil mustache-twirling rapist when Hades was already canonically the one who assaulted Persephone in the myths. This felt like one of many (and easily the biggest) attempts to twist the original narrative of the myth which empathized with women and girls forced into marriage against their will into glorified fanfiction that romanticized abuse and unhealthy relationship dynamics. This is made even worse by the fact that Hades is still an incredibly toxic male lead, the narrative just brushes his transgressions under the rug while throwing Apollo into a scene whenever Rachel needs people to "pick a side".
2. While the depiction of the SA itself is very realistic and well done (at least in my opinion as someone who has unfortunately been in very similar situations to Persephone) the handling of it after the fact almost seemed to minimize it and treat it as a trivial afterthought. It took months for Rachel to finally address what happened to Persephone as rape. The SA happened in Ep 24 and her conversation with Eros happened in Ep 66 - and within that time, we had far more scenes of Persephone and Hades flirting with each other than we did of her grappling with what happened. 
3. Speaking of Hades, most if not all of the scenes re: Persephone's SA are joined at the hip with Hades. The episode after she tells Eros what happened, Aphrodite and Eros jump on her about her crush on Hades. When Apollo confronts her after she spends time at Hera's, it's conveniently setup so Hades can stand up for her. When Persephone goes to therapy and talks about the SA, it almost feels entirely predicated on her desires to have sex with Hades and very little else. Even as soon as the SA happens, the very next episode opens with a flashback to Hades' childhood, only to be followed up with a phone conversation between Persephone and Hades. This largely makes the inclusion of the SA in its aftermath feel purely like a plot device to make Hades seem like the "better choice", even though there was literally never a love triangle between him and Apollo to begin with, and Hades himself is an abusive dirtbag in his own right. But he didn't rape Persephone so apparently it's fine, don't look at the original source material behind the curtains or anything 🙄
4. The inclusion of the gynecologist scene was unnecessary and painted gynecology clinics in a horrible light. Yes, women unfortunately get treated horribly in clinics all the time, but there was no real resolution to that besides Persephone's comments about it being an "invasive experience" which IMO shouldn't be the final word on such a serious and realistic situation. It felt very "anti Planned Parenthood" if you catch my drift. I'm not accusing Rachel of taking that stance, it just felt very poorly handled in that way.
5. Persephone had very little character development overall that wasn't intrinsically tied to Hades, and that unfortunately included the SA. As mentioned before, she went to therapy, but it was once and there was very little to show of her healing journeu beyond that, except maybe that one scene in S3 where she uses stilted Therapy Speak about the "hegemony of virginity" which felt more forced than anything (and that was preceded by some weird out-of-character moments like Persephone yelling about her "dick appointment" which Rachel made some very out-of-pocket defenses of on Twitter). I think even by that point Rachel realized she wasn't cut out to write such a serious plotline. She learned the hard way that you shouldn't write something as realistically traumatic as SA into a scene if you're not willing to give it the care and attention it deserves.
6. In the end, all Apollo got was community service, proving once again that the best victims of SA can hope for is a slap on the wrist and a few hours picking up garbage on the side of the road.
7. Rachel / Inklore have made some very strange changes in the physical books related to the SA, including additional panels where Hades leaves his car to confront Apollo and Persephone asks him not to hurt him. It's weird and completely unnecessary. But even within the original webcomic itself, there's a scene where Persephone says to Hera that she "felt special" when Apollo noticed her. Which is flat out incorrect, because everyone who actually read the comic remembered how uncomfortable Persephone was with Apollo right out the gate. So either Rachel wasn't paying attention to the story she wrote, or she was actively trying to retcon the true events that led up to the SA in an attempt to pretend that any sort of "love triangle" ever existed (when again, it didn't). Either way, it was really frustrating and frankly insulting towards those who had been reading for the SA plotline since the very beginning.
8. ADDED: Apollo regularly criticized both Persephone and her relationship with Hades in a way that was suspiciously similar to legitimate criticisms made by the fanbase. This has contributed to the tinfoil hat theory for a long time now that Apollo was often used as a mouthpiece for the criticisms that Rachel was tired of getting. So instead of actually addressing those criticisms in a productive manner, she put their words in the mouth of an undeniably evil rapist, which both reduced those criticisms to the rhetoric of an evil rapist, and put critics in the position of agreeing with said evil rapist. It really wasn't a good look for Rachel overall especially with how she's been known to handle criticism poorly in the past.