Was the ‘puffball’ actually growing ON the plants themselves, or just IN the hay? When those bales get and stay wet, they can sprout all sorts of fungal-y things.
The best thing to do with fungus/mushrooms growing in straw or wood mulch is to just disturb them with a rake, or pluck them out and toss somewhere HOT and dry so they’ll die.
Anytime you have ‘warm and wet’ fungus can show up.
Yes, I had a number of little mushrooms growing at the start. The puffball on the plant was what made me concerned however. It was spreading from the hay onto the thyme. I didn't want to use the thyme because I had no idea of the toxicity of the puffball. And, if I do it again this year do I need to do some sort of "fungicide" around the dead bales to prevent it from happening again?
I thought the point of hay bale gardening was to have a "warm and wet" growing zone. (sigh) I'm so bad at this!