There is nothing
inherently unreliable about the bundle file; when the subject of potential bundle file reliability has come up before, I've asked if anyone has ever saved a bundle file, then re-loaded the bundle file, and not have it work. So far, that hasn't happened. Even in your case, if it opened once, then it was saved properly. Maybe check that the folder locations for audio samples are correct? (The "busy" problem can also happen if a computer can't find the audio interface.)
However - I see no value to bundle files since per-project folders became available as a way to save projects. A bundle file is like a zip file in the sense that if one bit gets dropped or there's an issue with the storage medium, the file will likely be unreadable. If you save a project folder, then even if you lose a few cells on a memory stick or your hard drive sheds some particles and one of the files becomes corrupted, you can still recover the other ones.
I hope you didn't lose the project but if you use that particular memory stick again, I'd recommend re-formatting it. Although it seems solid-state memory sticks
should be reliable, I've collected a zillion of them over the years due to receiving them as press packages at trade shows. Although the majority work fine, several have failed, so I use them for temporary backup only and never as a sole backup...mostly just for file transfers, which seems to be your main use as well. But I'd recommend transferring a per-project folder instead of a bundle file.