Plot hole: Joy and Sadness are stuck outside of the control center. They are trying to figure out how to get back, and encounter maintenance workers who are discarding old memories. The maintenance workers show that they have the power to send memories back up to the control center to be played. Why couldn't they send the core memories that Joy had back up the same way? Better yet, why not use that method to send Joy and Sadness back up to the control center? The director of the film is even aware of the plot hole, and said "Yeah, well then we wouldn't have a third act," before explaining how the idea of recalling memories was added in later, "box[ing] [the screenwriters] in a corner a little bit."
Suggested correction: Even if they do send the core memories up to headquarters, they wouldn't be able to get joy and sadness through the tiny gap that the workers send the memories up. Joy has to be in headquarters for Riley to be happy.
This mistake is large enough that the director is aware of it. I think that more than qualifies it to be on this site.
Suggested correction: Joy is a control freak, she wants to return the memories herself. She doesn't even imagine that the workers can do such a thing.
Plot hole: In the beginning, vampires are shown to be invisible in photos but then they seem to appear in videos like security footage and social media posts.
Plot hole: Plankton replaces the secret formula with another message in a bottle, but later, when Spongebob catches him, he is replacing the bottles again.
Suggested correction: No, he is not. It might appear like he's about to do it due to the way Plankton and the bottles are similarly positioned as in the shot mentioned before, but there is nothing that indicates that he was about to repeat the same action. He had only picked up the bottle with the secret formula that he had pushed off from the pressure plate, he was then surprised to be caught by Spongebob so he accidentally knocked over the bottle he replaced the secret formula with. Also, when he accidentally knocked over the bottle, he didn't place the bottle he was holding on to back on top of the pressure plate to disable the alarm since it would mean returning the bottle with the secret formula back to its original spot.
Also, when it shows it when it happens about a few days or so ago, he doesn't knock it over.