Well, Synthesyzer says "400/400 x Matter replication gel" in "Cerebral Substrate" recipe, but it highlighted red like its not enough. I have setup where CUBE generates that "Matter Replication Gel" once (4k of it), becomes dormant and passes to "Cerebral Substrate" craft. I expected it to be a closed system where 4k of generated gel will be consumed by 10x "Cerebral Substrate" crafts, but the last 400 of gel could not be consumed.
Theres just a pipe between machines to pass the "Matter Replication Gel", no pumps used.

Looks like its just a factorio's bug, but mb not?

Floating point rounding errors. This is known Factorio issue with fluids and require specific setups to circumvent. The easiest is: directly connect fluid output with fluid input. The easiest solution: make 1 extra craft of gel out of sequence. Maybe storage tank will be required if cube does not want to go into gel's synthesyzer after such step.