"A red dot at an imaging location denotes that there was an image that was processed but it did not have sufficient overlap and/or matchable features so it was not included in the output."
The the overlap looks good overall the section that didn't turn out is right over a large section of moving water. There was a good amount of glare on the surface in a lot of the images which confuses the system's ability to match features.
These images were taken at solar noon which is why you were getting so much reflection. This can be addressed by using a circular polarizing filter to cut down on the back reflection or by mapping 1.5-2 hours off of solar noon on sunny days.
Sometimes I can't believe how much fisheye there is to the lens on the Phantom 4 Pro RTK. What were they thinking?