Mr. Stenchy - S1-E4
Continuity mistake: The second time that Jumba shoots Gantu with the orange string that wraps him up, the highest it gets is his shoulders, however, when Gantu falls to the floor, the string is now in three ringlets above his forehead.
Clash!! Sonic VS Knuckles - S1-E5
Revealing mistake: Right at the end of the episode, when Amy is telling Knuckles he should apologize, Amy has two right hands.
Plot hole: It's revealed at the end of the episode that the reason Tommie was sleep walking was because he was so nervous about the 5th grade test. However, he was sleep walking before news about it was given (ie: The beginning of the episode).