I'll try to search for the clipping files. It's been some time, and I don't remember exactly what it was. They did play perfectly in other players.
I do remember the offending song had a deep sine wave bass. The issue sounded like non-saturated clipping, integer overflow.
It drove me crazy, because at first I suspected my bluetooth headphones, etc. I tried to reset VLC completely, reinstall, tried to reduce levels below 100%. But nothing helped.
Edit: Couldn't find the files for now. I'll make sure to send them to you once I find them.
VLC 4.0 will get gapless audio and a different audio management, that will improve the quality.