Sorry folks, but you are now going to witness an extremely venomous reply to this question. Switch off now if you don't want to read it!
How absolutely ignorant can you be, if you have already bred from your bitch twice surely you know the rudiments of dog breeding, well obviously not. How could you leave an entire dog with a bitch in season, what did you expect to happen, he would say 'I can't mate with you because you are my mum'?
Fortunately there is very little likelihood that the pups would be deformed, although very closely inbred. In some cases breeders deliberately do this mating, if there was a good reason to do so, such as a very small gene pool.
Also if she was in season in June I would have thought she would have given birth by now, as the gestation period is only 9 weeks. Even if it was the end of June when she was mated she should have whelped by now.
For your dogs' sakes, get your bitch spayed and your dog castrated.
And don't come back on here asking who the hell I think I am, or giving some sob story, because we have heard it all before and people like you give decent dog breeders a bad name.
End of rant.