The Krabby Patty That Ate Bikini Bottom/Bubble Buddy Returns - S8-E15
Continuity mistake: At the beginning of Bubble Buddy Returns, right after SpongeBob reads the letter from Bubble Buddy, Gary's swirl is blue and his spots are red.
The Krabby Patty That Ate Bikini Bottom/Bubble Buddy Returns - S8-E15
Other mistake: Mr. Krabs pours Sandy's growth serum on a patty. It grows, and Spongebob scrapes some off to construct individual patties from the larger one. The larger one then continues to grow, but the individual ones do not, even though they are all the same meat.
The Krabby Patty That Ate Bikini Bottom/Bubble Buddy Returns - S8-E15
Continuity mistake: The giant Krabby Patty eats SpongeBob's shoe and sock in the kitchen. But by the time SpongeBob and Squidward run to the door and are stopped by Mr. Krabs, the shoe and sock have magically reappeared.
Answer: I believe this is the Season 6 episode "Spongicus".