When you have fry born with any form of retardation, you should remove them from the tank immediately, just incase they carry some form of disease( plus it is cruel to the fish).
My mother in-law made the mistake of breeding with abnormal fish and now she is having trouble breeding it out of her fish( 3 years later)
It isn't just the above, it is the fact that it will not look nice in your tank.
If you do want to breed guppy's I would suggest removing the guppy's that you bred with and starting with new one's just to be sure that it does'nt happen again.
I know I sound really blunt, but it is for the best especially if you would like to breed them!!!
Are you breeding with fish out of the same batch of fry?? because if you are that will cause majority of your fry to possibly be born abnormal!!
If you want to breed them your best option would be to buy several guppy's from different fish shops (only if that is convenient) that way you can be sure that your fish will be in no way related, which will lessen your chance of getting abnormal fry!!
Ps. I must say I have never seen or heard of guppy's being born with three eyes, very interesting!!
goodluck!
