It's random so you just had a string of bad luck. Let's not forget that completed military researches also count towards the fated 3 threshold, so if you want to maximize your chances, you have to also cut down the research in the military council.
Although I wonder what happens when there's no military tech to discover left. Does the budget for discovery get reallocated to research?
If that's the case you could really end up chasing after the clock, since there's 3 military techs in tier I.
At that point you could choose to defund your MC entirely if necessary and yes the game tries to shunt points around so they are not wasted, if it can. Research shunts to discovery and vice versa if you cannot do one of them.
OP the answer is bad luck and not understanding the quirks of the research system. Both understandable. I never set discovery below 60% for my starting EC (and I generally start EC, though some people swear by MDC as an opener). EC gets the lion's share of total funding. Depending of the research situation when prompted to open my second council, mostly MC and mostly I wait for the prompt, I will either equalise funding between the two or leave my EC getting the lion's share. MC is set the same as EC to start or possibly even more biased towards discovery. Continue until all core economic techs are researched.
Since adopting this strategy, I've never been locked out of energy generation and left in a crisis. I believe an option for T0 energy generation might be added, along the lines of the bio-fuel refinery, to solve this particular crunch, albeit very inefficiently.
On higher difficulties, military strength can be much more important so the above is only good for regular and below. Hard and Extreme require their own strategies.
Finally, in an energy crunch you can always mothball or lower production of less important buildings to ensure the core keeps going. You will never be locked out of construction because, as far as I am aware, energy is never used as a construction cost.
< Message edited by Laiders -- 6/12/2020 6:17:39 PM >