[The Fifth Horseman]

There are regular upkeep costs associated with base facilities, personnel and aircraft under your control.
These are deducted as soon as you receive your funding, meaning that if you expanded too much you can well start losing money each month instead of receiving anything.
My advice? Start selling off all the alien crap stuffing your base stores. You won't need as much guns as ammo if you're going to start using them in field.
Many alien devices from base raids can be sold off but for one unit (if you really feel like researching them). Same for alien corpses.
Also, if you have any Engineers, beeline your research to get Laser Cannons and start producing them en masse. Selling them off is a reliable source of income.