I think you're talking about where the side windows meet the door jam. This issue has come up before. You need to roll that L-shaped edge around 1/4 turn more to fit it in. It doesn't just flop in there and then get held in by the door. It should stay in even if you remove the doors! It's a Jeep
Here's how I do it:
1. Start the zipper about 2 inches and stop.
2. Start at the bottom of the L-shaped edge and twist it in so it's tight
3. Work your way to the top of the L-shaped edge.
4. Zip the rest of the way
5. Hook in the bottom plastic edge
6. Set the velcro
It's a REALLY tight fit and it's the hardest part of the soft top to put on in my opinion.
Hope this helps!