Rotor does not fit between pads after replacing the pads
Maybe the entire system was bled with the pistons not in its full retraction. So when you push in the pistons, you're actually just applying pressure to both the master cylinder and the diaphragm of the open system structure. (and compressing the air inside, if there are any)

Try opening the bleed port and screw in the oil funnel before pushing the pistons in. While you're at it, try to squeeze out any air that could be in the system. Then carefully plug the funnel, unscrew it from the port, and close the port.

Try squeezing the brake lever a bit but not too much and see if you don't have any sticky pistons. If they're stuck, you can follow this video: