I can think of two possible reasons. If the male was able to complete the act, then she was not pregnant; she's in heat. A tom cannot penetrate a female unless she is ready. She might have had a false pregnancy before. However, if the vet felt kittens or saw them on an x-ray, there's no doubt.
Of course, if the tom cat did complete the act, she could now be pregnant, if she wasn't before. Keep them separated, either way.
The other possibility is that she is due to have her kittens. Females cry and want your attention when they are due, and male cats are attracted to the discharge they have. I would isolate her from him, and just in case she is due to give birth, I would put her in her birthing box. If she cries for you, try to check on her as often as you can. I check for a thin, bloody discharge and then the mucous plug, and I would give her lots of love. Don't allow the male near her, regardless. He could cause an infection that could harm her and the kittens. Keep us updated, ok?