I have a problem with image alignment, let me explain.
From DJI Mavic Mini I acquired 550 photos in order to create the orthophoto of a fairly large area (about 70,000 square meters). Before proceeding with the flight I detected several markers positioned on the ground using a GNSS antenna.
The first thing I did was to create a chunk and have Metashape do the alignment of the images in order to get the scattered cloud (without using the markers). The initial result is excellent, only 3 images did not align (I am on the seashore and I expected that all the images taken on the water would not be aligned, instead only 3 were excluded). Subsequently I proceeded to place the georeferenced markers on all the images in which they appeared, then I relaunched the alignment by resetting the previous one. In this phase I gave both SOURCE and then SEQUENTIAL as a method to compare the differences. After these calculations the misaligned images are much more. Because? The coordinates of the markers derive from a topographic survey, so they are all correct and the points are assigned correctly in all the photos.
I wonder why without markers the alignment was correct, while adding them many images are no longer aligned.