Make sure that you:
-Did not use solid black or white on any frames for the gif.
-Did not submit the same file multiple times.
-Did not check the set transparency box on the upload website.
A theory I had was that there are too many frames in the gif causing it to glitch, but other people are thinking it could be the file size. I don't know the file size limit though. See this attached shield. It was something I made awhile back, but unfortunately did not upload correctly because it left a trail of frames behind it. The file size is only 6kb, but I used over 20 frames to make it.