It is not uncommon to have contact upon suspension compression of your aftermarket torque arm's rear mounting bracket and the floor pan on lowered vehicles and/or vehicles with an aftermarket rear end. The torque arm mounting pad on aftermarket rear ends is normally at least 1" more towards the driver's side of the vehicle than the stock rear end. This is necessary due to the larger center section sizing on aftermarket 9", 12 bolt and Dana 60 rear ends. The only solution is to dent the floor pan at this area for additional clearance or cut the pan out in this area and weld in a recess.
If you have a Ford 9" rear make sure you are using the set of mounting holes that are towards the driver's side of the car.