I just ran a nightmare mission and failed barely. When it said do you want to choose one of these options to raise your strength, I chose Combo to go see about finishing a combo mission. It wasn't quite cheap enough yet so I retried the level.
After finishing the first fight, I realised my timer was set to what it was at the end of my previous run! There was no possibility whatsoever of finishing in that amount of time, and you can only try these things 3 times per day. I've seen this happen a few times actually in various different situations; using the options when failing something can cause stats/timer to be leaked into the next game.