Bumper - are you able to post a pic of the fish you're unsure about?
Having had mollies in the past I have seen this behaviour and it is the norm. Firstly, you see it when the male is frisky - he can pester the life out of the female and get quite aggressive sometimes. You do have to keep an eye on the female that she's not becoming too exhausted as that can lead to stress illnesses or sudden death (that happened to one of my females - perfectly healthy one minute then after a couple of days of being harrassed by the male, she just suddenly went bully-up!). If you have a spare tank set up to use in emergencies for separating them, then that would be useful. I didn't at that time.
Also, another thing you will see is when the female is ready to drop her fry the male will constantly follow her around, knocking at her tummy, nudging with his nose etc - what he's doing is waiting for that first fry to drop so he can gobble it up! Oh no, they don't care that it's their own they are eating!
This is why some people who want to rear the fry, will remove a gravid female into a separate birthing box so that as soon as she's finished dropping fry, she can be removed and put back in the tank and the fry are kept safe.
If you saw something coming out of the "female" molly and the male ate it, it could well be that it was a fry. Did that molly look particularly rounded?
Have a look closely in your tank to see if there are any other fry. Sometimes they will hide out behind the filter, or in amongst plants/ornaments.
Regards, Athena