In order to improve the calibration, you could add manual tie points (MTPs) to better align the images and so the points in the rayCloud. The MTPs should be added in the problematic areas where there is for instance little overlap in the model or where you see misalignment. To know where to add a MTP, you should verify the re-projection of a point. Click different locations in the point model and check on the images (thumbnails in the right sidebar) if the point is re-projected at the correct location on all images.
How to add and mark MTPs in the rayCloud: https://support.pix4d.com/hc/en-us/articles/202560349
After adding the MTPs it will be needed to rematch and optimize the calibration of step 1. This means all subsequent results (steps 2 and 3) will be removed. For more information: https://support.pix4d.com/hc/en-us/articles/202558309