model number and/or pictures would help
is it briggs or kohler engine?
if its kohler then one of the top cover bolts goes through the air filter housing if thats what you are trying to do. if its just the filter cover then the stud can get stuck in the air filter knob and not unscrewing so the stud is unscrewing from the intake, if you keep going it will all come off enough to reach in and grab the stud so you can get the cap off
this is what the kohler looks like