Has there ever been any issues with tagging, ripping, or encoding, showing that at times any of these methods can result in a loss of Intergrity, most likely due to user error or bugs?
I'd like to know because some people seem to think there is no such thing as having any problems, which I find hard to believe when dealing with software.
Ripping, yes...there is a very high chance for errors. Encoding and tagging would most likely only damage files in the case of some kind of hardware defect or failure.
Yes. Always. In most cases, the user is the error. Sometimes, the programmer.
Also, lost user integrity is almost impossible to be gotten back. 
You can check your mp3 file integrity with something like mp3utility