is this supposed to be correct, i've been upgrading my legions base and the shield grids cost is deducted from the base funds but the defense modules are being taken from my own credits. i wouldn't mind so much but we have billions banked in the base and i have a little over a billion spare, and i don't have enough parts to get a commerce bay so i can withdraw the funds out from the legion base

I think all costs are taken from the player. I think right now it's because the Base can't store special costs, like EM and CTP. I think that's the way it's supposed to be, so you'd need to ask other players for help with the money.

as you buy modules, the money is pulled from your own credits
as you sell modules, the money is placed into base funds

if you want to get money out of base funds to cover what you spent, build a commerce bay