Magical-mutated blodd glows with octarine color when expossed to magic fields.
Huge mutations caused by magic require weak magic fields to cause mutant blood to glow but if mutation is barely noticeable an intense magic field will be required in order to make mutant blood to glow.
So, if someone is interested in checking the origin of a mutation, a "blood analysis under magic conditions" would be enough. But the trick is that small mutations require huge magic fields to make blood glow and people is afraid of intense magic fields because... well, can cause mutations so: what's the point of checking if this strong, fit and healthy-looking dude is a magic-mutant?
So, under your requirements:
A way that people can tell the difference between a child born with a mutation due to magical pollution and a 'natural' birth defect, some common trait that generally only shows when mutated by magic.
If someone wants to know the origin of the mutation, just get a sample of fresh blood and expose it to a magic field (a dark place would be better, to make the glow easier to spot) but if you're afraid of the effects of the magic field on your body it would be better if the magic field used is weak.
I want his companions to not realize he was a 'mutant' for some time, but eventually discover it.
Because exposure to magic could cause mutation, the hero and his companions would not get close to magic fields unless they don't have another option.
Because bleeding isn't (or shouldn't be) a common thing in a healty person, hero's blood wouldn't be freely exposed to his companions scrutiny unless something happened.
If eventually the hero and his companions are forced to go to a place with an intense magic field and they by chance get into a fight and some of them (including the hero) oh, by chance get injured with a bleeding wound... 227
and his blood starts to glow... well, they will realize.
Ideally I would prefer for the hero in question to not know he is a mutant either. [...] This means I need a 'tell' that, if checked, can help to confirm mutation by magic, but also subtle enough to be missed in this one hero.
How will he know his condition if he looks normal and he usually isn't bleeding near magic fields :) 183