I suspected that my guinea is pregnant but never knew how far along she was. I cleaned the cage one day and found two bloddy red balls with tiny black things that look like eyes - i'm assuming it's the newborns heads.
could it be a miscarriage or did the dad eat them ?
There is no way to know (you could have had it examined by a veterinarian), but I hope you are no longer housing a male and female guinea pig together. Breeding is very risky, and can result in the death of the mother or the babies or both. Please read: http://www.guinealynx.info/breeding.html
Also, I would add that if you suspect that your female is pregnant, it would be a very good idea to have her evaluated by an experienced veterinarian (one who routinely treats 'exotics' such as rabbits and guinea pigs) to make sure she is healthy and to help avoid complications.
Again, breeding - whether accidental or intentional - is so very risky and steps should be taken to prevent it from happening again.