As Frogboy has said, the wasted Social spending is not a bug, it's an intentional design decision because, as designed (with the automatic improvement upgrades), your economy goes crazy when you get improved buildings. My counter-argument to this would be: you can have the exact same issue the wasted social spending prevents with military spending (admittedly, the reason you're suddenly -1000bc in the red is more immediately obvious, because the game won't start ship production automatically). I would like to suggest two possible alternate fixes: a not so intrusive fix and a more radical one.
Tthe not as intrusive fix would be altering the governors: either prevent the governors from adding anything to the queue if the spending would put the player in the red, or give the governors the ability to pause production if the spending would put the player in the red, while the governor harasses the galatic government into freeing up funds for planetary improvment.
The more radical solution would be: instead of letting the player set spending as a precentage of total capacity, then subdivide that into military/social/research, let the player set research and industrial spending seperately, then allocate a percentage of industrial spending for social projects.
Another possibility would be to give the player a "head's up" on the economic screen (have the unused social/military points show up on the budget in parenthesis under the expense column, so the player knows how much they potentially owe)
Finally, completely on a tangent -- is there an official opinion on allowing us to adjust spending (and maybe even taxes if we're lucky) per planet (maybe on higher difficulty levels only)? I definitely want it. You know the AI wants it.