It's possible that this could be intentional for balance reasons, but it would be unintuitive. In vanilla, fish breeding, pentapod egg breeding, and iron and copper bacteria cultivation all give back unspoiled products regardless of the spoilage of the inputs. The bacteria added in Metal and Stars doesn't do this and instead preserves the spoil timer from the inputs. Since the spoil times can be very short, this can easily result in a bacteria spoiling practically immediately after being generated from cultivation.
If this is not intended behavior, the cultivation recipes could set reset_freshness_on_craft = true in their prototype like the vanilla cultivation recipes. Looking at the api docs, there are also preserve_products_in_machine_output and result_is_always_fresh, the former of which is used exclusively for biter egg harvesting, and the latter is never used and looks like it would do basically the same thing as reset_freshness_on_craft.
Not directly related, but catalytic recipes like the prior vanilla breeding/cultivation recipes generally also set ignored_by_stats and ignored_by_productivity on the ingredients and and products that are used as catalysts, so that the production graph and productivity cycles only apply to the difference between the input and output.
