If you were hoping they'd send ONE inquiry to Equifax but instead they sent ONE to equifax, ONE to trans union, and ONE to experian, you're SOL. That's within their rights when checking your credit. Afterall that's kind of the point of having three agencies - in case one doesn't have totally up to date info there are two others to fall back on. I know that my credit card company checks only equifax. Discover, on the other hand, does trans union. My mortgage lender did all three. It's just how the chips fall whether a lender sends an inquiry to all or not.
But remember since a credit score is attached to one bureau if you have a score of 700 with all three and each inquiry brings it down by 5, that is PER bureau. So, 695 for all three - not 685 for all three. If the inquiry was made to only one you'd have 695/700/700.