Rough Engine when foot on brake

[Wots]

Recently had my flex pipe replaced. It took two repairs as the first time they put the new flex pipe in it elongated the exhaust and the muffler was hitting the rear bumper when stopping. After they shortened the pipe I noticed the car began to run rough, but only when I was at a stop with my foot on the brake.
If you put the car in neutral the roughness disappears, same if you drive it. The only time it occurs is
when you have your foot on the brake even if you are parked, in neutral, or stopped at a red light?

[fenixus]

sound like your engine mounts are shot. they may have actually caused your flex pipe to rip open (too much engine torque movement or when shifting gears) in first place. check your mounts before you will need another flex pipe.

[71Corolla]

If it's not the mounts, it could be a failing brake booster. Easy to check, disconnect the vacuum line to the booster and plug the hose. Set the parking brake, and shift through the gears. Be very careful when doing this, because you will have no brake assist! For extra protection, block the wheels.