There is a condition called "prolapse" that can be quite serious. Here's a description with a photo. Does it sound anything like your turtle?
Excerpt from "Austin's Turtle Page":
There are two types of prolapses: Intestinal and penile.
Intestinal Prolapse
This is most often, but not always, caused by ingested gravel. The gravel is eaten and when pushed to exit the turtle’s system, it becomes lodged in the intestinal tract and, when forced out by the turtle, it exits the body bringing the intestinal tract out with it. Another cause is an impaction in the stomach that is finally released. These are usually self-repairing, as the intestinal tract retracts back into the body once the feces are expelled. If not, see treatment below. And yet a third reason has yet to be determined. Believed to be secondary to an existing condition, it is uncertain why turtles will sometime have these prolapse conditions for unknown reasons, most times, repairing themselves shortly after.
Once this happens, the turtle must be removed from the habitat, as other turtles (as well as the prolapsed turtle itself) my see this as a food item and bite it, causing serious injury and often times, death. Recommended home treatment is to place the animal in a clean, smooth container (I use the bathtub) and coat the prolapse with either granulated sugar (dry sugar, not a water:sugar solution) or honey. This will assist in reducing any swelling and hopefully allow the prolapsed item to be drawn back into the body. It is best to immobilize the turtle to prevent the animal from stepping on it, dragging it, cutting it, or even severing it while it walks and/or struggles. If it goes back in on it's own, that's great. If not, once the swelling has gone down, you can GENTLY try to assist it back into the vent. If you do not feel comfortable with this, it's not working out or you think there is possibly damage to the prolapsed material, then get the turtle to a qualified vet. The vet will assist the animal, sometimes surgically, in returning the intestines to their proper place. At times, removal of a section of the intestinal tract is required, especially if the exposed tract becomes injured. The vet will also suture a purse string to help prevent this from happening again.
Penile Prolapse
This is sometimes secondary to an existing condition, but sometimes it is just one of those things that ‘just happens’. When this occurs, the turtle should be removed immediately if housed with other turtles. I have personally witnessed one being bitten (yes, ouch) by another turtle, even though it was not in a prolapse situation. It is not uncommon for turtles to ‘display’ themselves for short periods of time or times of stressed, so do not be alarmed. At times, when retracting their organs, they may appear to swat or kick at it while it withdrawls. This does not mean they are experiencing a prolapse. If it goes back in, all is good.
With clean hands (preferably sterile gloves, but not everyone has these at their home), lubricate the organ with KY Jelly, and gently attempt to assist the organ back into the turtle. If this fails, as above with the intestinal prolapse, coat the penis with dry, granulated sugar or honey to assist in reducing the swelling. If the penis does not go back in on it's own, you can GENTLY try to assist it back into the vent. If you do not feel comfortable with this, it's not working out or you think there is possibly damage to the prolapsed material, then get the turtle to a qualified vet. Some conditions need some topical medication to assist in returning the prolapse, followed by a suturing which will be removed a few days later. Waiting too long or drastically traumatized organs may require amputation, but this is a very rare case.