Hello Alexey,
I have the same issue as timhemingway, and I am using photoscan pro 1.2.0.
The blue squares and black lines are not aligned with the surface, they are off-set...
This issue happen always when I shoot low orthos for higher final resolution ortho. It doesn't happen when I take high photos.
Overlap is 85% front, and 70% side.
How can it be fixed?