Binning can cause this issue, if at least one of the flats is binned differently than the others, or if the stack is binned differently than the frame you are trying to calibrate.
If any of the images are cropped differently you will also get the incompatible geometry error.
Also, since you are doing sky flats, there is a chance PI is detecting stars that you can't see. If it does, and the flats are not registered to each other, it will recognize this and refuse to stack the images because they are not registered (which is reported as incompatible geometry. Try star alignment on your flats if the first two are not the problem.