The scarcity of fertilizer was meant to be an economy balancer, so that players wouldn't just spam one upgrade and instead would try the tower-defense mechanics, but I think something I learned from this jam is if I'm going to arbitrarily limit something I have to be very clear about what you have to do to get more of it. If I had more time I'd probably make an enemy that spawns every level that you have to kill to get fertilizer, and maybe make a plant that costs 100 seeds that gives you 1 fertilizer, just to give options.
Thanks for the constructive feedback, it's very helpful!