You have a lot going on here... The biggest issue is that it appears you were mapping really close to solar noon which in the absence of a circular polarizing filter has made a really strong travelling sunspot. This occurs when the shadow of the aircraft falls within the field of view of the camera. If you look through your images quickly you will see a bright spot present in each image. This is bad and makes it really hard for the system to match features since they change from image to image.
Also, the second set of images is pretty overexposed compared to the first set.
When tall things are around they will get less overlap than you have prescribed unless you use the Ground Offset feature:
Mapping really tall trees is possible but it takes a lot of trial and error to figure out what works on different kinds of trees with different equipment. Mapping on a more overcast day would help to eliminate the hard shadows that are called out as something to be wary of in the Data Collection guidelines.
If you are going to be doing this kind of mapping I would highly recommend getting a circular polarizing filter, flying a bit higher using the Ground Offset feature and doing some small sample areas for free to check exposure settings.