Welcome to the Forum!

How's the water situation in Phoenix? I ask because the best course of action would be to drain the pool, pull back the liner so you can get under it to remove ALL the rocks and patch the liner from the underside where it is leaking. Then reset and refill the pool.

I strongly suspect that this isn't a viable option for you.

I'm thinking that there are probably more stones under the liner and they will keep poking through. Instead of cutting the liner to remove the stones, I'd just keep patching them (even double patching) and don't let anyone or anything mess with or abrade those areas (I hope you don't have an auto-vac!) [there is info here on patching liners]

Please keep me informed as to how your pool is doing - I'll help as much as I can from Maine