Can anyone tell me what's wrong with my turtles shell? It happened I think sometime after he was shedding and I tried to help him shed loose shell.

Looks like possible shell rot, or some type of fungal infection.
I may be off though.
I'd suggest scheduling a vet appointment

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"Nobody can do Everything, but Everybody can do Something."

I can't tell from the photos. Is the discoloration ontop of the shell or revealed after the shell sheds? It looks like it's layered on top of the shell, is that right?

Tell us a little about your turtle's set up. How big it is, how much water, filter, diet, and lighting. It might help us help you.

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My name is Liz
Do what's best for the animal, not what's best for you.

It looks like a type of fungus.
Then again it also looks like a layer of the old pieces of shell that are stuck on the newer shell.
Other people on here will be able to help you better than I.
Good luck with whatever it is.

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<3 Tessa

0.0.2 painted turtles (Mo and Squirt)
1.0.0 yellow bellied slider (Jebidiah)
0.1.0 Amelanistic corn snake (Rose)
1.0.0 Hog Island/Colombian Boa (Kah)
0.2.0 Colombian Boa (Jasmine) and her baby(no name yet)
1.0.0 Suriname Boa (Kayne)
0.2.0 Cats (Lilly and Reese)

I would have your vet check it out. And in the future I would refrain from "helping" a shed. That could possibly be what is wrong. It is possible you removed what was not ready to be removed causing a place for bacteria to grow. Best of luck and keep us posted.

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Ken
"Some people spend an entire lifetime wondering if they made a difference in the world. But, the Marines don't have that problem." -- Ronald Reagan