If your CR dropped from 70% to 2% after one fight, you did something very wrong.
Yeah, like take heavy damage, have low CR from damage and a couple of rounds of fighting (Pursuit after a decisive victory) and not have nearly enough room for the 1000 Supplies / Fuel / Loot that just dropped. If you lose enough Crew, this can quite easily happen, as the Logistics penalty piles on with the not-enough-Crew penalties, which are quite severe.
This is why I said I think that Logistics penalties should affect Burn, rather than suddenly crippling CR. It's not an intuitive mechanic. It's hard to see what's happened and why. It's also hard to react fast enough, in some situations, before CR has already dropped into the toilet.
Hopefully, the new explanation dialogs will educate new players to the point where this isn't a major hassle, but frankly, I've seen that kind of scenario happen, and there isn't any good way out, other than
knowing the mechanics work this way in advance and being extremely cautious on the Loot screen. Which is tedious, and, after beating a formidable enemy at great odds, very frustrating.