Here is how Pix4D defines Omega, Phi and Kappa: https://support.pix4d.com/hc/en-us/articles/202558969
Accurate geolocation and data for all three angles would need to be available for it to be taken into account during processing. If this is available, the “Accurate Geolocation and Orientation” option in Process > Processing Options > 1. Initial Processing > Calibration, could be used. However, it might be difficult to achieve for ground based projects.
If we correctly understood, there are only a few images that are not oriented in the right direction. In this case, we would suggest to add a few Manual Tie Points (MTPs) and to Process > Reoptimize the project, which should help the images to correctly align. More here: https://support.pix4d.com/hc/en-us/articles/202560349
In addition, we would also check that there is enough overlap between the images (at least 75% frontal and 60% side overlap). Maybe increasing the overlap could help the reconstruction, as more matches might be found between the images wrongly oriented and the others.
If all images were oriented in the wrong direction, we would add an orientation constraint: https://support.pix4d.com/hc/en-us/articles/205360385