Hi Scott, Welcome!
Can you post a picture?
Did you install this job? Are you a pro or homeowner?
What did the stone look like before you installed it? (I'm sensing from your post that it's not installed yet.)
I have seen some limestone that still has chunks and clumps of deposits right out of the box. Some also have this film you're referring to (out of the box). If that's the case, I would notify the homeowner first. If approved for install, I would install, the use one coat impregnating sealer (some guys do this before install), grout. Do not allow thinset to dry on surface! Keep plenty of fresh water handy. After the floor is installed, consider having a professional restoration company finishing the floor. Review all of your options before installation begins (if you want to get paid and/or satisfied with the end results).
