Messed up saved files

So, I noticed when I saved a file, some things changed from when I reopened it. Like animate seemed reposition some drawing frames in places I didn't originally have them in. Like an object I originally drew in the center got moved to the right side. I'm perplexed on how this occurred, and I'm worried that animate might mess up more of my files in the future, so I would like to figure out what's going on.