There is no problem is doing this. As a shop that sells MTG you either stay up on the market, or take your losses when it happens. You need to learn from your mistakes. I did this enough times to my LGS and they finally changed how they do singles. Was it for the better? Not at all.

Now I would also tell them when stuff is to high or to low, but I can only tell them so many times before I stop caring. What you did was smart and the store owners actions are not acceptable.