2016 Prius C with no cargo floor?

There are supposed to be two large pieces of heavy duty styrofoam which are very precisely molded to fit over the spare tire and jack kit, which results in a level surface to be covered by the thin carpet mat. They are molded as left and right halves, and they have little cutouts to make handles for removal & installation.

If these are missing from your car, my first guess is that somebody got a flat tire and used the spare. If the car was full of cargo, they would not have been able to fit the styrofoam back in over top of the full-size dead tire. They may have abandoned the foam on the side of the road without realizing how expensive it was to replace.

Check now to see if they made any other mistakes- missing lugnuts, verify spare tire, wrench & jack condition etc.

I would suggest getting replacements from a junkyard. I'm sure a dealer could sell you new ones, but given that they are bulky, the part price is likely to be very high due to the cost of air-shipping large boxes from Japan.

Note that it's technically a safety issue- that foam is part of the energy absorber system to protect you from rear-end crashes, so it would be good to fix properly.

Congrats & good luck!