There are several scenes where SpongeBob's back is turned, and his identity is not shown in Missing Identity.
When Spongebob walks into the scene at the end of "Plankton's Army", he isn't wearing his Krusty Krab hat and in the next shot, he is.
There are several scenes where SpongeBob's back is turned, and his identity and collar are not shown in Missing Identity.
When Spongebob is retracing his steps, when he wakes up originally the alarm goes off. In the second time, he wakes up on his own.
Plankton should know by now that the secret formula is not in a book, but on a piece of paper stored in a bottle.