worms in the mud inside coop

If it has been raining a lot they are probably just coming up from the ground.

 

They could be something like fungus gnat larvae or nematodes (small roundworms that normally live in soil). Fungus gnats are caused by a small black fly that, like their name implies, feed off the fungus that grow on the soil. Both fungus and fungus gnats enjoy wet soil.

Nematodes are completely normal and are usually harmless. Their eggs may be microscopic and are so light that they even blow around in the wind, making them omnipresent. Fungus gnats are also harmless (if in small amounts) and are more of a nuisance than a problem to your plant. To limit the number of fungus gnats, let your soil dry out between waterings.

Here is a picture of fungus gnat larvae:
http://entomology.ucdavis.edu/faculty/pa...

Hope this helps.