Most probable reason would be that I ended up editing on the wrong machine while being offline or having it open on another one, so user error. But I don't know.
In any case, the only 2 moving parts were KeePassXC (I think, not sure when I moved on from KeePass) and syncthing. But most importantly, it was easily fixed every time, no broken file - which points me more into a syncthing diverge.
Otherwise, no, apparently no issues with kdx itself, or I wouldn't have been able to merge these problems. (which brings me to my pet peeve, a good working merge is missing...)