Hmm technically they should actually give you more upgrade currency unless there's some kind of bug i missed. Either way the upgrade system could be a lot more clear and probably needs to be redesigned. As it is now, the only way to advance the storyline is to get more compute upgrades. In other words, you need compute upgrades to discover anomalies. Anyway, as I said I'm sure there's a much better overall design for the upgrade system as a whole.