Peeper89 - I don't think that is op's view, she is worried about the chickens unhappiness in their run and is feeling guilty that the birds seem unhappy about staying in the coop/run.
My suggestion is to improve the run, add bedding to the run, such as old hay or straw, pile it in deep, and they can scratch it up. Add multiple levels to the run, adding perches, pallets or old chairs or ladders to the run gives the birds more exercise using the vertical space.
Chickens really don't feel unhappiness unless you have them severely over crowded. If so, you might need to cull some, to better fit your set up.
Mrs K
My suggestion is to improve the run, add bedding to the run, such as old hay or straw, pile it in deep, and they can scratch it up. Add multiple levels to the run, adding perches, pallets or old chairs or ladders to the run gives the birds more exercise using the vertical space.
Chickens really don't feel unhappiness unless you have them severely over crowded. If so, you might need to cull some, to better fit your set up.
Mrs K