I was thinking of other suggestions, and I think this suggestion might be a good idea(?).
In my playthroughs of the game, I realized you could just upgrade one of the surrogates a bunch and basically have an infinite supply of credits to do anything with. I think a way to stop this is by having two separate credit types: Individual Credits and Station Credits.
Individual Credits and Station Credits are earned through the same way (making babies lol), but individual credits only work for that specific surrogate (meaning you can only use those credits to buy upgrades for that specific surrogate). Station Credits can be used for other things around the ship (if there's anything that takes credits that isn't surrogate-specific, like purchasing new surrogates).
There could also be an exchange rate between the two types of credits.