Jeppe
Do you have adequate overlap (~70%) on the images in the southern half of your project?
I know "go back out and capture more images" may not be welcome advice for THIS project, but in the future, if you have projects like this where the images look very similar (parallel rows in an agricultural field) it is VERY helpful if you can fly your project normally, then (or first) fly to maximum altitude and capture the full project at low resolution over the full site, and process all together in one project. (recalculate a new set of flightlines for the high altitude overpass)
As noted in my other response, it's also recommended to always use ground control - I think that would help in this project as well, presuming you have adequate overlap and can find some approximate ground control from the imagery basemap.
Cody B