I don't know what you mean with "getting punished for not completing the wrong dungeon." If you queue RDF, you're assumed to be up for doing whatever comes up, there being no "wrong ones." If you want to queue for random, but choose, it's on you to deal with cooldowns that might be the price of that choice.
While bugs should be fixed, one thing doesn't erases the other. When you consider these changes were part of retail, they also were the fixing of bugs. I didn't play retail at the time, so I don't have first-hand knowledge, but people who did have confirmed the cooldowns existed, even if they don't recall specific details on how they worked.
It was said that the effect of these changes is being watched closely, so that might mean that constant bugs in certain instances (as in, that dungeon is always bugged at some point, not a bug that happens only occasionally, which makes it harder to narrow down a cause) could get priority in fixes.