A method and apparatus are disclosed. In an example from the perspective of a User Equipment (UE), the UE triggers a first beam failure recovery (BFR) associated with a first cell. In response to the first triggered BFR, the UE triggers a Scheduling Request (SR) for Secondary Cell (SCell) beam failure recovery. In response to deactivation of the first cell, the UE cancels the first triggered BFR and the triggered SR for SCell beam failure recovery associated with the first cell.