I think the main thing that bothered me, from what I remember, is that he supported Ymir's ambition by carrying out the king's will, whom she loved, despite the fact that the king was a manipulative, abusive piece of shit, and it comes off like abuse apologism. I think there was something about how doing this somehow set her free from that, but it didn't seem like enabling her desire to carry out the king's will was the right way to do that. What makes that particularly bad is the manga painted it as it was somehow noble and it just made me feel all kinds of ick. I might have read a fan translation so maybe something was lost/misconstrued there, but it made it a little harder for me to accept the ending as a good one.
Anyway, I'll probably catch up on all the last bit of AoT anime I skipped so far and see if that is the case or if they framed it better. Still overall love the series. And am happy with an "Eren did bad things" ending, just didn't really like the framing of it from my read.