Making a cut at intersection between lines does not align the new points.

Very seldom had this problem before and then I could always see where i didn't align things properly but now when cutting a line at the intersection of another (with cutting tool) it almost always happens that the points are not aligned and when joining it creates a patch inbetween instead of just joining the two point to one. What am i doing wrong, any setting or is it an faulty update? I ran the 28.0 version

1: cutting with cut tool at the intersection. (the pointer says intersect here were I cut only it changes to path when pressing cmd for printscreen) 

2: the circle cut off is deleted and the intersection joined

3: moving one point after join command and you can see how its a not one but to points. 

thx!