Most sheds or outbuildings are constructed with a floor of plywood over 2 x 6 floor joists. This "floor" is set on the ground or on cement pads, leaving a space of about 6" between the ground and the bottom of the flooring. Bees only need a gap of  1/4" to gain access to this space. They usually go unnoticed until the colony is well established. The bees and comb must be physically removed. Block the entrance and they will find another way in and out. Spraying may kill a few but there are 20,000 to 60,000 bees under the floor. Un-removed comb will continue to attract  new infestations. Removal is the only answer.

The bees entered a     gap between the joist and the floor board.

Make sure there are no open spaces under your shed. Build or place your shed on poured footings making sure there are no gaps. Caulk all gaps with an exterior latex caulk. Sheds on the ground should be surrounded with 1/8" mesh hardware cloth between the floor joist and buried into the ground. Makes sure there are no spaces where outer joists connect. Caulk all gaps.