Why does Mouser put random parts in bubble wrap?

If they run out of one size of box they use the next size up - rather than make you wait. Weight is the major component of shipping costs, cardboard isn't so much. I once had two TQFP32 package microcontrollers arrive in a large box (big enough for a pair of boots!). They happened to be in a pair of waffle trays https://www.antistat.co.uk/jedec-waffle-trays/ (presumably they had some spare and had run out of other anti-static bags/boxes), hence a larger box was chosen.
 
I buy enough parts to notice that the packaging at Mouser is really dependant in the person doing the picking. They decide themselves, I am sure with some guidelines what extra packaging to use. It can get excessive but on the flip side they provide most of the packaging materials I need to use for my shipments