Ah, I'd heard of the basemap feature but never used it.
Yes I suspect there could be issues with your markers as they appear to be duplicated.
In 'Smear1.png' you have two markers both called 'point 25'.
In 'Smear3.png' you have three pairs of markers:
- Point 56 and point 56
- Point 59 and point 59
- two markers both called point 24
Maybe you merged chunks and didn't merge markers for points 24 and 25, and Points 56 and 59 wouldn't merge anyway because of the difference in the letter 'P'.
I couldn't say that this was certainly causing your issue, but it can't be helping.
The fix for that would be to go carefully through all the markers in the reference pane, and check for any duplicates. Each time you find a duplicate rename one of them by appending something like "_DUPLICATE" to the name (leaving the original part of the name intact, i.e. "point 24_DUPLICATE". Then for each duplicate marker, filter the photos by that marker and go through them replacing the duplicate for the other one, until the 'duplicates' have no projections listed in the reference pane, and then you can delete them.
Then you would need to optimise again, and rebuild your orthomosaic.
Make a backup first as it could be that I don't know what I'm talking about.
The replace marker feature is shown in the attachment in case you weren't aware of it. It is only available in the photo view (it just looks like the 3D model view in my screenshot because my input images in this example are 2D images of a 3D model, which might be confusing...)