is there suppossed to be a cover on the brake light switch on the end where the arm meets

What brake light are you referring to, the rear tail lights or the brake light on the dash? Honestly, replacing the front brakes shouldn't do anything to the brake lights. However, if the brake fluid got low, it could actuate the interior light.

the rear brake lights stay on. the brake fluid level did not go low. no other warning lights came on. unless the fuse or the brake light switch is removed or disconnected, the lights stay on.

It sounds like the switch itself is shorted out inside. If the lights are on all the time, the switch can't be opening the circuit.