Marking Status of Reference Books

I have just realized from discussion and this blog that reference books are being "marked as used" from the reshelving cart. I'm not sure when this survey began, but I was not aware of it.
As a reference librarian, I frequently go over and reshelve books on that cart when I am not busy at the desk, in order to become more familiar with which books are being used.
Another source of wrong data for this survey is the cart of newly acquired reference books which comes into the reference workroom and then goes out to the shelving cart. I just this week emptied this cart of new books directly to the shelving cart....apparently these books would be marked by someone in circulation as having "been used", when they really had not.
I'm sure we can think of easy ways to work around these two potential data problems, but first we need to continue working on the communication issue.
Yvonne