Although most wetsuits are lined for comfort, you can irritate the skin by remaining in your wetsuit and getting in and out of the water. This can cause tender, reddened skin that often has the appearance of a rug burn or abrasion. It may also cause hair follicles to become infected.
Your description sounds more like this could be due to sea lice or jellyfish larvae. Areas of the body that are usually covered by the swimsuit or, in your case, a wetsuit, are typically affected. You may have kicked up larvae swimming through the seagrass that became trapped under your suit. They are then free to attach themselves to the upper layers of skin, where they cause the symptoms you mention, as well as itching.
The condition usually lasts a week or more, or until the body can get rid of them. It is best to thoroughly rinse yourself after your dive in areas known to have a sea lice problem. Avoiding areas with reports of sea lice infestations is also a good idea until these areas are clear. Staying in your wetsuit for prolonged periods seems to invite the problem.
There is no total protection against sea lice, but avoiding exposure will greatly reduce the chances of contact.