Forgot to ask if your gear selection light works correctly. As you move the shift lever to a different gear, does the light move to the correct gear?
It's possible someone had the cover off and did not get the light sliding mechanism over the shift lever. This would push the light mechanism up under the cover at the back popping up the cover. If this is the case, you need to fix this as soon as possible, because you're damaging the light mechanism. You can't buy parts for the cover. You have to buy the entire cover.