It was probably just loose screws and the cover was vibrating. Reinstall it and check that the screws hold in tight. If they're not, fill them with glue and some toothpicks, redrill the holes (the bit has to be as thick as the center of the screw, so that just the threads dig into the wood) and reinstall the grill.
If the vibrations persist, that means something else is loose. Try first with the screws that hold the metal chassis. Check for loose speakers, too. Then try the screws and nuts that hold the transformer, PCB, etc. These should have thread locker and not be loose, but if they are, clean it well with thinner and reapply some thread locker.
Only do this if you have experience and know what you are doing, and the safety precautions you have to take. Don't think you know, read safety precautions when working with electric equipment. The safest bet is to take it to a tech.
Also, removing the cover changes the sound of the amlifier. It should sound more bassy. It doesn't have tubes, so it shouldn't be a big deal, except that you should keep it for resale.