Continuity mistake: After Brian finds the note Alf left, we see William put the note under the microscope to inspect the tear drops. When William says "I'm going to go find him," he stands up and we see him leave the note on the microscope. When the camera cuts to William walking through the door, he all of a sudden has the note in his hand that was left on the microscope. (00:12:55 - 00:13:35)
The End of Flutter Valley (3) - S1-E3
Continuity mistake: When Reeka is conjuring the fake rainbow to distract the Flutter Ponies, the grey pot on her head is blue for a while.
Monster in the Playhouse - S1-E9
Revealing mistake: As Reba the Mail Person exits the Playhouse, she goes past the window, and you can see her exit the sound stage through a door painted the same as the background.