Recently, I tried upgrading a few farms with food bonuses into manufacturing plants, and I noticed after a while that my max population was only decreased by the base amount, not the entire amount. Reloading fixed this problem. Also, is the entire population supposed to disappear after the next turn? I figured the population would just take a huge morale hit as it went down gradually.

This may or may not be related to a 0-production bug I encountered a few games ago. I built an antimatter plant (+25% manufacturing) on my manufacturing capital, which also had a factory/bonus, and the planet would not produce any social or military after that. Reloading also solved that problem.