Illegal Substitution???

[FSCoach]

HS Game: Man on First no outs. Visiting team pinch hits. Pinch Hitter checks into the game with the Home Plate umpire. The pinch hitter is wearing uniform #13.

The pinch hitter bunts and the runner from first to second is retired at second and the pinch hitter is safe on first base.

The home team (in the field) points out to the umpire that there is already a #13 in the game and that the situation should be treated like a batting out or order or illegal subsitution. They claim, that they have no way of telling if the new hitter wasn't the other #13 who had made an out in the previous inning.

(There really are 2 different #13's on the bench at the start of the game but no official rosters or lineup cards that would make that clear before the start of the game.)

After some discusion, the umpires call the pinch hitter out and now have two outs in the inning with no one on base.

Did they make right call?