It is not possible to craft fertilizer at the moment. The plant material and guts are properly consumed by some percentage, but the fertilizer is just not there. A problem similar to disappearing tanned leather at the beginnings of 0.62 stable.

I made sure that there is room for fertilizer in the barrel, but nevertheless I carefully checked around in case it popped out.

I've checked it with both small and regular piles of guts.