you trapped her way too early... this can bring on huge stress and cause them to abort , if you have a read through some of the pinned topics, you will get to know when she is ready to drop, then ( if you must) net/trap her , mollys are quite good at resisiting the urdge to eat theyre fry, so long as there is a lot of cover in the tank and mum and the othersare well fed, the rate of survival should be quite high, these fish are also prone to stress induced illness eg,whitespot etc, so id be carefull when it comes to *interferring* .. if i was you ( and i have learned from exp) i would be inclined to let her drop in her own way, time and then try to catch fry from the main tank
hope that helps, there are bound to be variations of opinion,but thats mine

, you`ll find what suits you /her
shelagh xxx
oh, and good luck with the fry