From what I can tell, it seems like it's a problem with both the pencil tool trying to act smooth, and the fill bucket not picking-up completely on the blur the pencil made. Haven't used that program before, but I wonder if there's a way to both decrease the blur on the pencil tool (or the ability to use different brushes), and/or increase how much the fill bucket is able to pick-up. Even then there's also the problem with you not being able to easily flip between frames as quickly.
Not an iPad user unfortunately, so I can't give you proper suggestion or alternative. Best I can do is use what I know from using programs like Krita and Gimp, or look online for other options like Animation Desk, Flipaclip, or Wick Editor. FlipaClip being the most popular option.
~~~
Though, I think despite these troubles the little animation still turned-out pretty good. Love the little smear frames on the wings, and the cute smile.