How does Google employees waiting at bus stops cost the city money?
On the one hand, they generally don't cost the city money; but it does give tech shuttles a free pass at using city bus stops that, if you or I stopped at (and were caught), we'd have to pay a fine.
On the other hand, they do cost the city money in that that can (and do) delay the actual city busses from stopping at the stops and, as the adage goes, time is money. (The slower a bus goes, the more potential overtime the city will have to pay and the more busses the city will need to use for a given route to maintain the same headway.)