A lot of tagging programs add them as they just get appended or prepended to the file regardless their content. Sometimes one program reads a format but writes in the other, I have personally found a FLAC in the wild with ID3v2 at the front, ID3 at the back (corrupt) and FLAC metadata as well. The FLAC metadata inside was wrong, the valid one was outside at the front (sadly it was a broken JIS encoding).

There is no sane approach to media. Between legacy formats, legacy tagging, and all kinds of implementation specific bugs, you are in for a ride if you want to cater to more than one decoder out there :)