Well, I'm a Control Systems engineer (although not aviation). I program systems. The unusual and unexpected ways in which software can 'fail' (although it actually just does what is told) is immense, and more likely the more complex the programming. There is also the possibility of code corruption, caused by external factors such as electrical variation/surges, short circuits and so on
But for a moment, let's assume the software has been programmed perfectly, tested to the n th degree and we have redundancy built in.
The software can only act on information fed by other systems, sensors, signals. On a complex installation there are thousands of inputs/outputs, some virtual (internal software values) and some generated physically. For some of these I/O, under certain failure modes, the computer will not be able to tell if a signal or variable is true, or in some cases which of multiple signals is giving the 'real life' value if there is a mismatch. In the case of a major fault developing (e.g. Control panel fire) the computer may lose some or all of its I/O.
This type of issue in ground based transport could simply cause a stop and shutdown scenario, but of course that's not an option available for aircraft.