I rehab turtles and I had a wild mud turtle come in a couple years ago with dark pin holes on its plastron so I took it to the vet and he did some scrapings and said they were from bacterial infection. I cleaned the area daily and kept him dry for most of the day only allowing an hour soak. The vet had me give him a number of antibiotic injections. Depending on the drug used you may need to do the dry period after the antibiotic phase. Some antibiotics are hard on the kidneys and the turtle has to be kept well hydrated. Topical treatment alone usually isn't enough because the infection is usually systemic. I strongly recommend you take the turtle to a knowledgeable turtle vet. Don't wait to see if it will get better. Advanced shell rot can kill. I also had a wild RES come in with pitting on his plastron but these ended up being scars from a healed infection. My opinion is that wild turtles probably have stronger immune systems than captive ones and can many times fight off infections they may get without human intervention.
Gulf Coast Turtle and Tortoise Society

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