Will bad camera calibration affect pixel coordinates?

I believe the answer to your question is to answer how to perform a better camera calibration.

Quoting from Calib.io enter link description here:

• Choose the right size calibration target.
• Perform calibration at the approximate working distance (WD) of your final application.
• The target should have a high feature count.
• Collect images from different areas and tilts.
• Use good lighting.
• Calibration is only as accurate as the calibration target used. Use laser or inkjet printed targets only to validate and test.
• Per sample, proper mounting of calibration target and camera.
• Remove bad observations. Carefully inspect reprojection errors.
• Obtaining a low re-projection error does not equal a good camera calibration. Be careful of over fitting.