2007 Honda Civic brake pads

Not normal, how are the slides? This is where the bolts go thru, also, the calipers, if fully collapsed should allow the remounting to be easy, there is not much room with new pads and new rotor, but force is not needed to reassemble. Either you have the wrong pads, or the caliper needs to be replaced, try opening the bleeder screw, the piston may go in a little further. If so, you might consider new calipers. The other thing is if you used the old rotors, the rust ridge on the inner and outer edges could be hanging it up. Try new rotors.

The piston and seal is what the concern is, not the casting. Sludge builds up on and behind the piston, and this is what causes frozen calipers. You will be seriously overheating the brakes. This can cause the brake fluid to boil, and cause brake "fade" and maybe loss of braking altogether. You really should figure out what the Hang up is. Did you put new rotors on?