Does Toy 'R Us (or more expensive-than-average) retailers have more extra parts than average?
The number of parts shown on the box of the LEGO set indicate how many parts are included without the spare parts. Spare parts tend to be added for the smallest pieces of a set that can be lost easily.

Spare parts tend to be fairly consistent between identical sets regardless of where they are sold and sets with a greater amount of parts will generally have more spare parts.

I wrote to LEGO customer services, here is a quote from their response.


  When it comes to spare parts, it is random what pieces are included in
  which sets.  We always want to make sure our fans have a little extra
  to go with their awesome imaginations.
  
  LEGO Direct Consumer Services