I can think of actually quite a few, though keep in mind that I don't think all of these are bad:
"Fear of a Krabby Patty" - I like the episode, but it's not one of my favorites of season 4 and I feel like there's a bit too much screaming in it.
"House Fancy" - I don't hate the episode, but I'm shocked to see how much people like it on here. Most of it is dull and unremarkable, and I'd forget the toenail scene is even in it if people wouldn't bring it up so much. I agree that people are probably overreacting to that scene, but is the rest of the episode really that good? Looking at Squilliam's house gets too much focus and isn't that interesting, and I don't think Squidward winning automatically justifies the episode being good.
"No Hat for Pat" - Just because Pieguy likes an episode doesn't automatically mean it's good. No one talked about this one or thought anything of it until he praised it, and now people like it. I don't hate it, but it's a typical unremarkable post-movie episode that isn't very interesting or memorable.
"Chum Bucket Supreme" - I never understood why people tend to like this one so much. I think it's pretty forgettable and it doesn't stand out amongst other Plankton episodes.
"Squidward in Clarinetland" - Very weak first half, Clarinetland is kind of cool but it's not in the episode too much and I feel like it could have been more interesting than it was.
"Enchanted Tiki Dreams" - I don't think this one is too overrated since there are some people who have similar feelings to it like I do, but I feel like this one could have been a lot better. The first half is annoying and boring, and the second half, while interesting and nice, isn't too special or memorable overall. I'm fine with Squidward being happy, but can there be more to it than just that?
"Love That Squid" - I think this one is quite annoying and boring, and I fail to see why people like it. Once again, Squidward winning does not automatically make an episode good.
"Perfect Chemistry" - I don't hate it, but I think it's completely unremarkable and the idea of a Sandy and Plankton episode could have been much more interesting than it was.
"Treats!" - The only thing that stands out about the episode at all is Gary constantly meowing, and for me, that isn't necessarily a good thing.
"Plankton's Pet" - I like it and I'll agree with the majority that it's the best of 9A, but it certainly isn't top-tier Spongebob material and since 9A standards are pretty mediocre, that's not a huge compliment.