Here are my two guesses -

a) Use a finer file, and as wide a one as you can find. The finer the file, the shallower the cut, and that makes it easier to just get the high spot.
There is a skill to filing a flat, you have to feel the contact area as you file, and move the file so the centre of the felt spot remains on the spot (which you also can't see) that is high; and that the plane of the cut stays constant. Sometimes I mount the file in a vice and push the part along it, especially if I don't want to mark the part by holding in the vice.

b) if you file too much the unthreaded end of the pin will poke out the hole and if you get it just exactly the right amount wrong the pin will lock the crank and the nut tightens as usual but it's not tight enough to ride.

And if the cotter is the cheap kind file it enough to get rid of the plating on the flat.

AND grease the pin. Somebody will want it to come out sometime.