The one case I'm aware of where a software glitch did cause a plane crash, there was pilot error compounding the problem. Air France flight 447 was an Airbus A330 flying from France to Brazil, and while high over the Atlantic, the software recorded inconsistent data in its airspeed measurements. (The official crash analysis team concluded that the inconsistent data was likely due to ice crystals blocking the pitot tubes on the plane). The inconsistent data made the autopilot disengage. Pilot error then caused a stall. One pilot then tried the correct move to recover from a stall, pushing forward on the stick to nose down and regain speed. The other pilot was pulling up on the stick to stop the dive, not realizing that that's exactly the wrong thing to do in a stall (or more likely forgetting his training due to panic; he had a lot less experience). The flight software, receiving inconsistent inputs from both controls, averaged the inputs, resulting in zero change in pitch. (It also sounded the "Dual Input" alarm, but the pilots were too preoccupied with their own controls to figure out what that meant at first, and by the time they figured out what was going on it was too late to recover before the plane hit the water).

https://news.ycombinator.com/item?id=4224707 has some discussion of the events, including the fact that the control design (where each pilot has an independent stick) was part of the problem. On a design like Boeing uses where both sets of controls move together, the experienced pilot would have noticed the less-experienced pilot pulling up on the stick because his own stick would be moving, and he would have said "No, nose down." And if they had nosed down to recover speed while still high enough in the air, they almost certainly could have regained control of the plane and saved 228 lives (including their own).

So in retrospect, I think my first sentence was wrong. The software did not glitch, it did exactly what it was supposed to do. It was pilot error that caused the initial stall, and multiple pilot errors that caused the failure to recover from the stall.

There may be examples of software error that has caused planes to fall out of the sky, but I don't know of any. The only plane crashes whose cause I know were due to hardware failure or pilot error, usually a combination of the two.