I used my first colony ship on a PQ 16 planet, and the next turn the cost was 6B while it was taking in 3B.
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You are likely running on 100% spending. A planet on 100% quite often costs more than it provides.
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Contrary to other 4x games (like civilization), spending aren't related to income. So you can spend more than what you earn. The tax rate has an influence on the tax income from each planet. The spending rate is how you utilize the capacities of your planets. So it is normal at the beginning of the game to spend more than what you earn. After all, you have 1000 BC in the treasury.