I dont think you’re giving enough information for a proper solution. I’m not very familiar with Krita per se, but this could be an artifact left by a sharpening filter, or more likely a result of a paint bucket or magic wand selection. Those dont do well with edges that have blended with the underlying color.

All of these can be avoided by using different layers for these overlapping elements.

I figured out a fix in the end. It was pretty much exactly what you described. (ps, since it’s kind of a stupid question should I delete the post?)