I just found out what has been happening by cricinfo commentary:
21.5 Mahmudullah to Umar Amin, 1 run, OUT, driven to long-off for one. Bizarre scenes here. Not quite in the spirit of the game. He has completed the single, goes back to the other side of the stumps because Mahmud is bowling round the stumps. While doing that, however, his bat is in the air, and Mahmud whips the bails and appeals for the run-out. They go to the third-umpire, and they can't do much once the team appeals. But common sense anybody?
Two over later:
Replays show Mahmud whipped the bails off in routine manner, but Shakib at midwicket noticed the bat was not grounded, and appealed. Mahmud wasn't quite sure what was happening.