Great, now the game'll never be finished.
Seriously, it's more a case of old mistakes coming back to bite people on the butt again.
In the case of the FP system, I can't think of any good way of creating it beyond telling the players "GM fiat - this is the way the system works". Part of the problem is that it makes the shop seem like it has an infinite amount of supplies, instead of a limited amount that must be rationed based on who's assisting the most. Maybe if the characters themselves weren't aware of the actual numbers it would make more sense; the players would have the numbers, but the characters would be getting "um... do you think you could go out and do something for the rest of us?" instead of "you're short 100 FP". Note that bartering skills should affect the results - if applied by dint of actually having a conversation with the shopkeeper. You CAN use your GM powers to declare it like this... not sure what the players would think (comments?).
You could also start keeping track of the shop's inventory, and make characters aware of it ("Can I get 3 more clips of ammo?" "I'm sorry, I've only got 1 left."). The problem is it adds one more layer of complexity to the GM's job; you'd have to add in more supply-gathering missions and the ability to trade supplies in for FP. And players who are on more frequently have more opportunity to get that limited inventory, unbalancing the game slightly.
The sudden end to the Slime Breeding Den isn't so easily fixed. It makes being captured seem easily fixable ("I get captured, and Shiva will rescue me the night after!"), instead of a fate to be avoided at all costs. It interrupted several character developments (Azure getting comfortable with the slimegirl, Azure getting Kali released from the wall if not outright rescued, the slimegirl growing from a simple rapist into a more complex opponent). I thought about complaining when it happened, but then I thought "it's not my game, I'm not even playing, let's see where this goes". I can't think of any way of fixing that right now.