I always spot the moments where they miss colouring a certain part of a character. An example is in "Through the eyes of a spiketail" where I think they do it twice.
In the same episode, they manage to un-sync the characters lip movements a couple of times.
And don't even get me started on how aweful the character models can look sometimes. As Vek pointed out, you get hilariously bad drawings of the characters tons of times.
I've noticed one strange thing. Of all the characters, Ruby... who is arguably the most complex and detailed looking character, is drawn well almost all the time... where as Spike and Littlefoot seemed to look different in nearly every other scene. I don't know, maybe it's just me...