I really like Krita, but I do take issue with it's default settings for the fill tool, which sometimes don't respect boundaries in the way one might expect.  However, sometimes simply clicking 'limit to current layer' can fix this issue, or when that fails, adjusting the threshold to be lower.  Both of those are in the 'Tool Options' box in the lower right hand corner.  Having those options allows for a lot of useful things that aren't easy to do in other software, but the way they are set to work by default can be unintuitive compared to a lot of other paint software.