Looks like a dowel... they're there to help line up the cover and stop it rattling about. When you remove the cover, sometimes they come off with the cover, sometimes they stay in the crankcase. You need to ditch one of them. If you have tightened the cover down hard, it may be difficult to extract but you should be able to pull one of them out with pliers and this will probably wreck it for future use. Luckily, you have a spare
This is a great way to remove hollow engine dowels without damaging them:-