Also I just noticed that when upgrading ships it doesn't take into account the amount of strategic resources you'd be freeing up by doing so.
For example: I have a ship that requires 2 Durantium, but just acquired an extra 2 Durantium and so wish to upgrade my ship to the new design which requires 4 Durantium. The game thinks I don't have enough Durantium to upgrade to that design, so I'm forced to decommission the ship and then rebuild it instead.