This is an error I've been dealing with for years. When you build framing on a level then add horizontal bracing (any diagonal member connecting in the 90 degree space between two perpendicular beams) the beams never join correctly. The most consistent fix for this is to pull back the diagonal, snap it to one of the two perpendicular beams, then snap it back to the intersection - then it seems to understand, but it still breaks down quite a bit, and I'm forced to fix this by dragging the handlebars that control the extrusion.