Well, after only 2 years of owning my 2010 R56 CPR S, my oem filter would look like this. There were two leaves in the bottom of the box under the filter and sand as you can see in the corner. One leaf was stuck in the filter itself.
Got my K&N drop in filter from Out Motoring today, great service btw and accepts international CC's. A+++
I can actually hear my turbo spool up a bit more and the violence is back when I mash the pedal heh heh heh.

 

The stuff you saw in the box was stopped by your filter... it didn't go through. Intake air moves upwards through the filter, and the box holds anything that the filter doesn't let through. So the leaves, sand, etc. are pretty much normal.

Spridget