I see you miss the quest as it not bug. Check my hint below and hope it can help you.
After you beat RURTBORO gym, talk with the professor in front of the gym. He wil ask you to find the guy who stolen Decon Scope. Now go to route 116, go in Rusturf Tunnel. Before go in the tunnel, talk with the old man in front of the cave to taken quest (he will ask you to save his bird). Now go in and beat NPCs in there Magma and Aqua team. After that talk back with old man for finish quest. You need finish this quest, before can go talk with Mr. Stone. Mr.Stone will give you letter to send it to Steven.
Go route 104A, find the house and talk with the old man (who ask you save his bird), and then ask him to go Dewford town.
Check this guide also:
Oh okay. I did what you told and I can not reach the trainers in Rusturf Tunnel. There are rocks that require Rock Smash in able to pass by and I do not have that yet. What do I do?