My team and I at work are all having these issues (4 different computers, all with the same issues):
I am working on projects that have multiple file formats: Apple Pro Res video files, .jpgs, .psds, and built-in generators. When I use transitions (specifically cross-dissolve), I will later come back to work on the project and the material that was cross-dissolved may be missing in some spots and not in others! I have to go back and redo all of that work, as it does not come back!
I am also having issues where, upon reimporting .jpgs that I've updated, the file looks as if it's in the timeline, but it will not appear in the viewer (it's invisible!)
These are things that I hope are addressed in 10.1.2, because I'm spending hours fixing all of these errors and am seriously considering going to Adobe Premiere or something.