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Mining/research station has 1 energy upkeep, so I imagine that's what is reducing the visual deposit size by 1.
no, this is happening as soon as i build the outpost, before i even build the station

Are you a bulwark vassal OR playing Knights of the Toxic God origin?
no, neither one. but i thought bulwark gives me basic resources anyways, it's a subsidy not a tax?

You probably have a negative energy credits modifier

Which is also what the post above me is asking
i am neither a vassal nor knights of the toxic god, what other things could give me a modifier and where do I find it?
 
Any penalty to income applies to the displayed values of deposits under your control. You see the same thing with AI, in reverse: all their deposits are significantly higher than the value displayed before the system is claimed.
 
Even without relevant modifiers, deposits sometimes change their listed output. This happens when building the outpost sometimes, others when building the extraction station, sometimes not at all. I have no idea why this happens.

It's extremely annoying when trying to find appropriate spots for Dyson Swarms, because it makes the displayed output untrustworthy.
 
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Federation taxes. This is not listed anywhere in the game and is the most common source of this. I only learned about on the wiki after going through the same kind of hunt years ago.
omg lol i didn't even know there WERE federation taxes. kind of cool that there are, from a roleplay perspective, i just wish it was listed somewhere. that tracks tho, thanks for solving the mystery.