It seems the not aligning images are the ones where there is only litte of the object or background visible.
Therefore, RC has little to go on and I am not surprised.
What you can try is add ONE Control Point per image that does not align.
Sometimes, that helps.
Or you try raising the max features per mpx to 20000.
Type “yellow triangle” into the search bar and you will find the answer - it’s nothing to worry about.
Would probably work with the green rectangle as well - you need to cover the basics yourself with the help and forum!
I think they give you the number of tie points with the selected camera…