Rust returned on car..?

So i have a 2001 Pontiac Grand prix that has some rust coming through near the underside of the car (mostly around the bottom of the doors and such). So a few weeks ago my dad and i attempted to fix it by: sanding off all the rust, filling in the holes with some goop stuff from autozone, then applied some black paint that was supposed to keep the rust from returning. the can said to wait 3 days before applying primer and paint. so we did just that and after 3 days applied the primer and then after a few days, applied paint. So it was looking all good until a few days ago, i noticed that some rust was coming back through. WHY? so if you can offer any suggestions on what we did wrong or what we can try differently..please let me know :)