Alright...um...I accidentally deleted my save game about an hour ago (850 years got to ~3050), while looking into this, so these partial screenshots are the last records of my first game of Stellaris....

In the first partial screenshot I have 97 star-bases but can support 96. Star-base upkeep is 142.41 (25% over).

In the second partial screenshot I built 106 star-bases as a test, which completely wiped out my Sectors Income as well as added the star-base upkeep penalty (478.69 - 250% over).

If I build a number of star-bases in-between (for example I tried 101, or 5 over), then I still have some sector monthly income but it is drastically reduced.

I know my first post I thought I had found a bug, so I thought I would ask someone with more experience if this is the case, or a mechanic in the game I'm not aware of....

...and now the sense of losing my save is starting to weigh on me....

You might've. Hard to be sure. But, my first guess is that the starbase cost is applied to the relevant sector, and therefore reduces Sector Income of your Budget. Starbase Upkeep then covers the starbases in your core systems, I think. By the way, going above starbase capacity gets ludicrously expensive. The +25% or +250% cost penalty is applied to every single upgraded starbase, and also to every single unupgraded outpost, and also to every single module on any starbase, and also to every single building on any starbase. At least according to the wiki.

I certainly noticed the loss of income, which is why I stayed at most 1 over; I figured that the cost being shown was the per star-base cost rather than the total, but the numbers don't add up there (ie 478.69 * 106 = 50,741) .

As an experiment I actually removed all of the sectors, and my income went to -29,000 or so, all of the planets were actually making negative values! (I guess that is because of the planet limit...but still it was amusing to see).

If I was to take a guess at what is happening, maybe it's increasing the upkeep for everything (buildings, anything that uses credits for maintenance), not just starbases.