I doubt she has missed a hole in the webbing for 3 years, this isnt a duckling.
Holes in webbing is very common, was at a ladys house today and as we were going threw the babies picking me out some, we kept noticing holes in a lot of the webbing. She asked if I knew how they got it as SHE DIDNT DO IT.
of course I do, I've seen it a million times. It's from stepping or running over sharp stuff on the ground. They are tuff little membranes, but the right object, at the right angle will go right threw it. I have also see them get into fire ants, 2-3 ants will eat a hole right threw it while they are bedded up on the ground.
Small holes that arent healed will often heal over and close up on their own.
Sounds like this one is permanent though. Once they have healed, they will not close up any more. Happens all the time, it's just hard to see a little hole in the webbing, 1 we never look at the feet, 2 if we did we couldnt see it if you didnt pick them up.
Happens more often that you'd think, but is no big deal.
toe punching is a common method too for breeders, but is usually one distinct round hole pretty big and close to the toe not out in the mid webbing section.
Each breeder does it a little different, but that's where most put them.
My bet is injury from stepping on something though, nail, wire, screw, broken glass sharp rock or stick, all sorts of stuff that can pop right threw there.
She'll be fine though dont worry