I don’t see what the grid has to do with anything it’s not part of the PCB just an alignment aid. The one I did up there was 3 mins in KICAD directly, are you sure there were no stray lines. When you load 3D view it will tell you exactly where the issue is.
That’s exactly the problem. The grid is an alignment aid, and if the grid is set incredibly small it can be nearly impossible to align the points because they will keep snapping to the grid.
I recommend upgrading if possible — there’s some relearning involved, but KiCad 6 is really an improvement. (And needed if you want to open someone else’s KiCad 6 projects.)