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Welp, the answer is quite simple

Take more images. When using multiple images in multiple poses, a better intrinsic matrix can be calculated.

So two steps :

1. First image is the main image and is used to determine the x,y,z axes for all the cameras (so one image visible by all)
2. More images for each camera. This will improve the estimation for the intrinsic matrix and in turn will improve the projection of 3D points to the image