Your instinct is correct. That super bright roof caused some big changes in the exposure times for the immediately adjacent trees. These tree images then don't match up at all with the images of just trees. The system tried to put it together but it didn't work out too well.
Dealing with roofs is really hard in general but adding trees into the mix is even worse...
This is a case where using a fixed exposure time that will show OK detail on the root and in the trees will be needed. In Map Pilot you would need to use the Manual shutter mode. No matter what though the images will have to be a compromise due to the hot white roof and the dark surrounding trees.
We will grant a one-time refund for this issue since you did a great job of trying to identify the issue on your own.