You are correct that Gigalith learns Stone Edge at Level 48. There are two reasons why you didn't see Gigalith learn Stone Edge: 1.) You probably just gave up teaching your Gigalith the move. If you go to the move relearner and give him/her a Heart Scale, you can reteach the move to your Gigalith. 2.) It already has the move as part of its moveset.
The 1st reason is most likely the case in this scenario.