A person who actually has clue what they are doing will look at the content label to determine what is in the tank. The O2 clean sticker identifies the tank as being suitable for O2 service. The nitrox bumper sticker is merely intended to keep people from accidentally grabbing a tank that they shouldn't use. Since we're talking about doubles, that doesn't seem particularly likely.
What is by far the most troubling aspect of this issue is that the fill idiot (he doesn't deserve the lofty title of fill monkey) shut off the isolator. The worst case involves an OOG situation. Its much more likely that the diver would end up on a boat, or at a dive site, when they discover that they got a bad fill and that they have half the gas that they should have received.
Whether the shop fills nitrox is not relevant. If they can pump hyperfiltered air, then they should have filled both tanks. If they can't, then removing the O2 clean sticker after checking with the diver would be appropriate. But to fill only one of the cylinders is absolute, unmitigated idiocy. Its also ineffective, since the diver would, hopefully, have opened the isolator when they found that (i) their primary wasn't working; or (ii) their SPG read zero.
There's no question that the shop in question should be avoided until they get their act together.