Continuity mistake: When the two children visit the Ghostbusters the little girl is wearing a pink pajama top and pink bottoms. In the next scene the pajama bottoms change color and are now orange.
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.
Cygnus! Hyogen no senshi - S1-E3
Continuity mistake: When Hyoga punches the hole in the ice, the area around it is mostly clean from any debris, but when he returns there are chunks of ice scattered all over the place. (00:06:30 - 00:08:00)