Okay, so when I add metadata ( album cover, artist, etc) to a mp3 while its being played, it adds a small ... i don't know.. a scratch kind of sound, a interference. in the mp3 file.
So, whenever I play that song again, I can hear that sound at the same position (If i saved the metadata when the song was at 2:34, it creates a permanent mark there)
Is it only me? How to i fix it?
see e.g. here: /t/14751/1
Editing a file while playing is definitely a bad idea. Depending on the padding, the file has to be re-written, the pointers of the player could then point to a completely different block which messes up the sound.
You should check your files for integrity.
Understood, but what about the spoiled files? Can I fix them?
What is checking for integrity? and how do i do that?
I don't think that you can fix the files. Which program should guess what the audio was like before it was overwritten with garbage?
Checking the integrity can be done by various (freeware) tools: mp3val, Mp3diags, foobar2000 (the utilities in the context menu).
Mp3val has a scan mode that gives you a first impression how many files there are with problems.
Mp3diags lets you look into some more peculiarities.
Foobar2000 ist quite nice for rebuilding VBR and CBR headers and streams.
I tried Mp3val, it has the option to fix all the errors.
Thank you very much. 
Yes, of course it has an option to fix errors.
But you did not tell us if Mp3Val found your specific errors and whether ist was able to fix these.
It said "the file may be corrupted at the end". And after fixing, I didn't see those scratches anywhere, go I guess, yeah.
But this 1 error is still persistent.
I don't get what the error is, since the seek is working fine.
I think you can mend that with Foobar2000 and the utilities context menu where you can rebuild the VBR stream and header.
Different tools are good at different disciplines.
I like to use foobar2000 as the first choice, this minimizes the need for a second tool. 
DD.20170323.2008.CET
Very rarely, considering the amount of audio editing and tag changing tasks I do, I stumble upon a file that at the very end has a popping added to it; which for 110% was not there when I first edited any of those files [well maybe in few of them, but not in hundreds through the years]
But I have no way of proving that Mp3tag is to blame, as it is so rarely find out by me [sometimes I do not hear it but see it in the editor, as it is very small insignificant change at the end, where flat line of silence is suppose to be]