I am not certain, I believe to a certain extent it is genetic. If you hatched out a batch of chicks from assorted breeding groups and all had crooked toes then yes probably an incubator issue. But if you only get 5 our ot 80 hatched most likely a genetic issues passed on in those birds.
I purchased some Australorps this year and although they are beautiful birds I have more than half with crooked toes, is it an inbreeding issue? Most likely. This fellow has had these birds for many many years, and most likely has some inbreeding going on. So I am selecting the bird without the crooked toes to continue on in my breeding pens for next year. Although some may argue you do not eat the toes, these chickens have to have good feet in order to free range and roost properly, so I am all for straight toes!
I have also read before that too much protein early in life can cause toes to go crooked, as well as a cold brooding floor. So one cannot rule that out either, especially if you havent raised the birds from day one. But if you raise all your chicks the same way on the same floors and same food, then the crooked toe ones were definately predisposed to it in my opinion and should be taken out of your breeding pens.