For one thing you have moisture coming in from the outside through the block walls.
See all that white stuff on the blocks, that's effervescent, not a good thing.
Fine to lay a vapor barrier, but the water coming in from the outside also needs to be addressed.
Most common reasons are there are many, is mulch piled up against the foundation holding in moisture, no working gutters, downspouts not far enough away from the foundation, flower beds forming ponds.
That brown stuff it may be fungus, also a very bad thing, it feeds on the material that holds the wood fibers together.
If it was mine I'd be spraying it with Bora- Care with Mold-Care.
https://www.domyown.com/boracare-with-moldcare-p-1265.html
Far cheaper to treat it now instead of having to replace the floors later.
Any exterminator company can also treat if you do not feel like doing it.
Those rocks are not going to hurt any, just make it more painful to crawl around on.
I most often see what your seeing because of a lack of proper venting.