Season 1:
Look Before You Sleep (I really didn't like Twilight in this episode)
Over a Barrel (kinda boring in general)
Owl's Well That Ends Well (way too predictable)
Season 2:
The Mysterious Mare Do Well (everyone seemed out of character, especially Scootaloo, I didn't think she would ever just abandon Rainbow Dash like that)
I loved all the episodes, but these four were basically the ones I disliked the most.