I am having similar issues.  I have not gotten one good stitched image from their camera so far, using DroneDeploy and also AgiSoft.  One issue I noticed, after the most recent firmware upgrade on the camera, is that they changed the default overlap from 80% to 30% to be more accommodating for their "quicktile".  It would have been nice to know about this change, rather than finding out after several flights that wouldn't stitch. 

They tell me I am flying too fast (using DroneDeploy for flight planning), but if I slow down, I won't be able to get more than about 20-30 acres per flight.  I have not yet tried this recommendation though. 

I am not too happy with their system so far.  AgVault has been nothing but a pain and does little more than organize the images, unless you get the paid version.

And just to clarify for one of the others who replied, we are not trying to align images here.  The camera is capturing green, red, and nir.