I'll remember to take a microscope next time we cut or buy.Which is why you should inspect any feed before you buy it. Properly made and stored hay should have none of these issues.

It's the nature of the crop, not really much to do with storage and harvesting.
Certain pathogens and mites live in the live plant which don't live in the stalks left after harvesting.
I have a field of cut mixed grass lying in puddles atm. Not an awful lot you can do about nature deciding to make life more difficult.