Did they give you the wrong tubes? Yes. (Well, at least probably.)
Will it matter? Probably not, but if I was you it would still probably bother me.
When I take long off road treks on the XR400, I carry one tube, a 80/100x21. I have installed that size tube in the back tire (a 110/100x18) a couple of times, and while it isn't perfect it works. The 21 incher is about the same as the old 3.00x21 size. The rear tire is about equivalent to an old 4.50x18. That's a bigger difference than you're looking at. So I suspect it would work and not cause you any problems.
However, that being said, if I was in your shoes I'd call the dealer and talk to them about it. Unless you're in a hurry to mount the tires they can surely order 4.00x10 tubes, and I don't know about you, but I'd feel better knowing they were the right size.
-kevin