It’s most likely dirt, but there is an alternative explanation. If the 3DS was never disassembled and the spots appeared seemingly out of nowhere then the screen *could* be delayering in a few spots due to moisture ingress and the discolouration is, well, mould. Hard to tell from your picture due to poor lighting. Google images of LCD mould and compare to what you’ve got on your hands. It’s a fairly common problem on certain devices, especially in humid climates.
EDIT: Oh, you have a screen protector? You’ll need to peel that thing off and see - it could just be trapped dust. I assumed this was just a bare screen - sorry, the photo isn’t great.