Gonna say that Hana almost hearing Miko's cry for help is a flag that they're supposed to be working together, so keeping her in the dark might have been a bad idea.
Don't know what to think about the spoiled offering. An anon said it might be related to
kegare, a Japanese term meaning pollution/defilement which is particularly important in Shinto. Reading about it, one of the causes is contact with death - in this case the spirits. So maybe the miko are angry with Miko for disrespectfully putting their offering in a place where it can be defiled, and are expecting her to somehow remedy the situation.
One of the wonderful thing about this manga is that it keeps us guessing about so much! Not knowing the answers to all the mysteries keeps me coming back for more, so I don't want everything to be explained straight away.