Has anyone came across an issue such as this and if so, were you able to fix it? We have noticed this issue on multiple flights
Hi @bsumner,
Welcome to the Pix4D Community 
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It seems that there might be a problem with the calibration in addition to a rotation of the project. Please make sure you have marked the correct GCPs and you have not inverted the order of some GCPs.
Please share the quality report with us.
Cheers,
Daniele
Hi @bsumner,
Thank you for the quality report.
How are the geotags of were the geotags created? Are you using PPK workflow and adding the geolocation in a second moment? It seems that images from the top part of the project got coordinates from the bottom part, and during calibration the position were “moved” to the correct position (increasing the % of differences between initial and optimized parameters).
This can be caused by having multiple flights where different images share the same filename.
Can you please verify this possibility?
Cheers,
Daniele