This has happened to me a couple of times. I've found that it helps to NOT have the camera locked on the Sim when they enter the cave. The camera attempts to follow the Sim, makes the Sim move to a weird position because of it, and resets them.
This definitely worked for me, as numerous dive site resets didn't.
I completely moved the camera away from the cave and just wited for the info panels to let me know about my sim's progress.
Have to admit I didn't realise they weren't working, I thought they were tunnels to the islands! duh!!
It was only when I realised they weren't registering in the skills journal, I thought to search the problem.
Thanks all for helping me resolve this