Yes, we would need more information on the stones; what are they, are they dry? Have you tried doing a small sample cast over these stones? I guess not.

The reaction (where the resin has gone white) is pretty extreme. This indicates either a significant reaction with something in the stone (moisture perhaps) or a physical action (were they particularly dusty?).

I know this is little help now (with the stones already covered) and so I almost don't want to say it but it is pretty important to test the resin over any substrate that's not already been well tested (like pennies have) to check that the appearance is what you're looking for and that there are no adverse reactions. Small plastic pots can be used to make a 'mini version' of your substrate/embedments and will give a good idea of what the end result will be like, as well as identify any reaction problems.