I was working on this model for 2 weeks there was no any problem, today I was simply trying to create a wall and create a window in the wall, so I’ve created a surface and trying to cut off the window in the surface it doesn’t work, just line not intersecting with surface, after I decided to divide surface into small section and suddenly its ripped into small triangles. I’ve tried to recreate the whole new surface but still same problem 
Upload the .skp file so we can see what you’ve got. It looks like you’ve cot some edges slightly out of plane.