If you go to upgrade ships, the cost to "upgrade all" is VASTLY larger then the cost ot upgrade individual ships.

This is easy to test...

1) Start a new game and buy a colony ship, dont move your starting one (incase distance has anything to do with cost)
2) End turn, launch colony ship
3) Go to the upgrade screen for the colony ship, click constructor. On my difficulty level it says 552 bc
4) Click "upgrade all". The cost to upgrade both colony ships on my difficulty is 1182

Some basic math...

552 times 2 equals 1104 bc
Doing the batch upgrade costs 78 bc more.

This is MUCH more noticeable if you have 20 fighters you want to upgrade (300 a piece compared to ~8.5k total) but is harder to control.

So all you people "clicking upgrade all" are ripping yourself off.

Possible reason why...

The function that calculates purchase price seems to be exponential....if X equals the difference in military costs between a constructor and colony ship, the debt is X^P. With 2 colony ships, the equaion is now (2X)^P. In english, 3^2 is 9 but (2*3)^2 is 36, an increase of 27 simply by doubling the base (adding more ships and therefore more total cost).

So the more ships you add, the more the price explodes because of how purchase price is calculated.

I honestly dont' know what the formula is so don't quote me on this, I'm making all this up. But it makes sense seeing how purchase price explodes...it definately isn't linear, otherwise a stock market wouldn't be so drastically more expensive compared to a basic market.