Hi @McKenzieBredemeyer , agree with @Pål_Herman_Sund , my guess is insufficient overlap. Would you be open to sharing the processing report here? It seems like some images were discarded especially in the areas with gaps in the ortho. Areas with tall trees and other elevated features are especially prone to this, as the target features (like the tops of trees) are much closer to the sensor than the ground is.
Usually increasing the overlap and/or flying at a higher elevation can improve that as it helps add redundancy in the dataset for tall features.
Do you recall if any defaults were changed when preparing the flight plan in ArcGIS Flight? What was the overlap/sidelap set to, and at what height were you flying above the terrain? You could check these numbers by opening ArcGIS Flight, opening the "Refly" list of flight plans and browsing to this mission's flight plan.