Took my 09' 1.8L into the dealer for the widow switch recall. At the sametime I had some warranty work done. I had been getting a whirring bearing noise when the clutch was engaged but went away when the clutch is out. Turned out that it wasn't the bearing itself but the throwout actuator sticking causing the throwout bearing to get stuck in an intermediate position creating a rattling sound. Seems that there is a TSB for this issue so if anyone as this issue with the car the solution may not require dropping the tranny.
2009 Vibe 1.8L Manual - DBW controller, Hydraulic engine damper, S/S brakeline retrokit,22mm solid Rear ARB, urethane rear coil dampers, Front strut bar with brake cylinder brace, PIAA 410 driving lights, PRM Intake Wilwood front brakes, Lexus hood lifts