Only the shop that replaced your heater core would know whether they broke open the A/C system in the process, but normally, they shouldn't have had to. The A/C system is a closed/pressurized gaseous system entirely separate from the heater core/radiator water-filled system.
If they did add freon to your A/C system when they were replacing your heater core thinking for some reason that it would help with the overheating problems you were experiencing, it's like RickOKC said, maybe they didn't properly use/read the gauges made for working on A/C systems and simply overfilled/over-pressurized the A/C system.
We can only speculate on what may have happened and who may have done what, but the important thing is that it sounds like your VX overheating problem has been solved.