Hello,
Im having problems with polygons not aligning correctly when using the Zmodeler bridge-two holes function.
I have tried to place the opposing vertexes more neet before bridging, but still the same problem.
any known solution? See the picture below. 
small_orange_diamond
do they have smae number of vertices?
I just tried bridging two cylinder(octagon) and found It happenend when I ‘drag’ mouse ‘right side(----->)’.
So try this
move mouse left side as you click 2nd hole’s edge. (make sure keep mouse button clicked while moving)
and move horizontal unless you want extra edge loops on connection