During the course of the adventure someone fails a roll, be it a roll to disarm a bomb, or reset the security system, or shut down the killer robots. But that doesn't mean bad things have to happen.
If the system you're using is player/story driven this failure might just means the story gets exciting. Failure in this case should just mean detour.
To illustrate, think of the story as a starting point and an ending point, with many paths leading from the start to the end. This failed skill roll means that we're on a new path. Perhaps with less time, or with new threats.
As long as the players know they can trust you as the GM they won't worry about failing a roll. In fact, if they know they can trust you, they'll be excited when they fail a roll.
This sort of trust comes from not being an adversary to the players. You hear this sort of thing all the time, about how some GMs are out to GET the players. That's one of the many reasons I hate people, but there are plenty of GMs who are the ally of the players, and are willing to let them fail and admit they failed so that together they can tell great stories.
I'm not saying there shouldn't be consequences for failure, there totally should be. But they should rarely be instant player....er I mean character death.