I've also had similar cases of this, If you look closely at the slot where the disc goes in on your console. There is a dust collector that the disc slides along as It enters the console. It looks like a thin strip of rubber.
What you need to do is, wipe that "very gently" with a soft cloth to remove any built up of Dust on that collector.
As Micky mentioned It won't affect your console short term,Though always try to keep It clean.
MyPS3 Miscellaneous
25/07/2009 / Sydney Northen Beaches, The Watcher