It's possible that the shop is confusing WTA with NET liquids. I had a run-in with a guy at a local shop about this myself. I explained it this way:
If you make a cup of coffee, you're making a coffee flavored drink with some caffeine in it. You don't have a cup of caffeine. If pure caffeine is what you're after you'd use whatever process you chose to isolate the caffeine from the coffee; the result would not look, taste, smell or be of the same physical makeup as coffee. You'd have a chemical.
WTA is the same type of animal - the result of extracting minute amount of individual chemicals from a sludge of tobacco leaves and discarding the rest, which is not a NET.
I don't know if NET flavored eliquids stain teeth but I was just pondering what could possibly lead people to make such an uninformed statement.