You need to be very careful when bees are in a chimney, especially if they are in the flue itself. If they have drawn any comb the heat of the rising smoke/gases from a fire cam melt the wax and start an instant flue fire.
When bees are actually entering a building interior space it's quite common to find dead ones all over the place...window sills being a prime spot. This doesn't mean that they have been sprayed, The bees are attracted to the light of the window or light bulbs etc. and work themselves to death much like moths do.
Scott