Hi Gal
In short 
The main issues can be pinpointed to not enough overlap and sharp angles. From the screenshots that I have seen I can say for sure the overlap is not the best. try to get to 80+% overlap to get better bundle stability ( alignment of the scene ) and I can say from my experience even misalignment gets away…
regarding ALIGNMENT settings, set these settings, then delete all COMPONENTS already in the scene and realign it again.
if it is a small sensor, I would recommend you to change the DISTORTION model from BROWN3 to Brown3-4 with Tangential ( any with TT distortion from the menu )
Alignment_settings.jpg