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.
Fenikkusu! Jigoku o mita senshi - S1-E6
Continuity mistake: Miho and Shunrey get back to the hospital room to find it empty. Bandages are on the bed, and they change position between shots. (00:10:25)