The job of the waveguide cover is to protect the waveguide (opening) and the magnetron from buildup of food particles and grease.
When the grease and food particles build up on and behind the cover, they will carbonize and arc - and maybe even flame up!
The solution is to clean it and keep it clean - but if it's too dirty or is burned, it must be replaced.
Sometimes it's necessary to remove the cover to clean both sides of it, and to clean the edges of the opening it covers.
It is sometimes held in place with a small plastic rivet (or screw) and once that is removed, the cover will slide over a little then drop down.
Be VERY careful not to get cut on the potentially sharp edges of the opening, and do not spray anything into the opening.
Apply an alcohol-based cleaner (such as the purple kind) and /or gentle scouring powder to a cloth or paper towel and carefully wipe it out, then when it's dry, reinstall the cover and the rivet.
I suggest to my customers that they NEVER use any ammonia-based cleaner (like the blue stuff) on a microwave, since the ammonia will crack and distort polycarbonate plastics.
William Miller † MicrowaveDisplay.com
March 2007