Thanks PROBERT1968, that gives some more clues.
Wooded areas can sometimes be harder to align due to (i) possible movement of the crown, and (ii) possible lack of distinctive features that can be used for matching between overlapping images.
If you take a subset which should cover one of your 'holes', how much overlap is there? When planning missions for photogrammetry (manned or UAV) a key consideration is the overlap, both in the direction of the flight line, and between adjacent flight lines (sometimes described as sidelap). Different terrain and end user requirements can dictate, but overlap of 70% or better is common. If you lay out your photographs in one of the problem areas, how much forward/sideways overlap do you have?
Can you post a pair of images (or extract thereof) and circle the area(s) that give you a 'hole'?
Also, as per previous message, can you detail which options were selected when you tried processing in PhotoScan?
Dave