im not sure how they got in myself, I dont think the stock airboxes ever seal very well, i remember on my Bonnie i would always find dirt and stuff on the wrong side of the airbox, and im sure many smaller particles have been sucked into the TB.

The stuff was all plant-based as i recall, and maybe it wouldnt do anything? but it just goes to show the potential for sucking large objects into the engine is always there, and the MAF screen could save your butt.