I don't use ISIS, but I do use Google Wallet pretty much anywhere I can. Everywhere I've been that has the sticker for ISIS and I go to tap, the cashier always says something along the lines of "Oh, ISIS doesn't work". I tap anyway, it works, they're surprised, and I tell them it's GW. I know Jamba Juice does NOT like ISIS at all. Rite Aid doesn't show they accept ISIS but GW always works there.
I have had times when NFC didn't work. I'd get the chime that something happened, but on screen it says "please check with cashier". Usually it boils down to the NFC attachment on the terminal has been smacked and broken, or a connection has come loose; at least that's what a manager friend at Famous Footware told me. He actually pulled it out from under the counter and showed me it was just a couple wires they hooked into their terminal and whatnot.
The only other time I've had trouble using it has been when the store uses an all-in-one terminal (like Jack-in-the-box) and they have that security cover on it to keep people from seeing your pin; for some reason, their security covers usually block the NFC so I can't physically get a good tap and end up using my card.