Metadata of Songs managed with iTunes
I doubt iTunes is directly involved. iTunes edits your metadata when you tell it to do so by using the built-in id3 tagger or the fetch cover function. iTunes updates other information like playcounts or ratings in a separate database file that doesn't affect songs metadata.  

I suggest the next time you see a such badly tagged mp3, you investigate using an id3 editor (eg Tag and Rename) : 


are the ID3v1 tags synchronized with the ID3v2 tags ?
if ID3v2 are present, which version is it? 2.2? 2.3? 2.4?
try to spot oddities that could confuse players : many covers embedded, huge size of the comment field, etc


So I suggest that it's one of those corner case that iTunes happen to process well and not your other player. But to answer more directly to your question, if you think that some process has altered your metadata, you can set the files as read-only to prevent any modification.