I've noticed that when you are in prone position and moving close to, or onto rocks, you sometimes automaticly go to crouch position.
Also when you are a diver and you get in shallow water, you will automaticly stand up.
To remain undetected you'll have to get back into prone position as soon as possible, but sometimes its to late.
My suggestion is that it should be able to "lock" your prone position, so that you'll never automaticly stand up/go to crouch. Maybe it should be default!
I get it all the time in the scuba showcase when moving to the beach near the base.
As for the rocks, try crawling over the rocks/near the rocks anywhere.
I think you should leave it up to the player if he/she goes from prone to crouch or stand.
Suggestion: If it's not possible to normally crawl on a rock, because the rock is to high you should be able to "crawl-climb" and and stay in prone position, when you are on top of the rock.
Suggestion: For a diver:
When you are in prone position, you will go from swimming to prone position.
When you are in crouch position, you will go from swimming to crouch when the water gets shallow enough.
When you are in stand position, you will go from swimming to stand position when you get to the shore.
Optional: you might wanna add an position icon/picture to the HUD, for when you wanna move from water to land as a diver (maybe only regular mode)