They could be aphids. The hop aphids are green or brown small, pear shaped insects generally feeds on leaves and cones by sucking sap. The aphids infested leaves exhibit yellowing, curling and wilting where as the cones become brown. Also this insects excrete honey dew, a sugary substance which helps in development of sooty mold (black fungal coating on infested parts).
I think in your case aphids might have been attacked the cones before harvesting. Drying the cones will generally get rid of most of the aphids.
Hop aphids (Phorodon humuli) on a hop plant