There are many possibilities, depending on the precise situation. It could
be as simple as a file format or as complicated as a standard which is not
really a standard. Microsoft ilkes to play with standards to keep the
competition off guard. There is no even playing field.

It could also involve proprietary technology. When I wanted to process
hundreds of photos last year at a local photolab, I could not because the
lab used Silverlight instead of cross platform technology. (Before anyone
corrects me, I know about Moonlight, but refuse to install it on principle.)

My point is that there are many barriers and we cannot generalize. If you
use a Mac then you could face similar problems, so it is not specific to
Linux. Everything is skewed towards Windows and ignorant techies in
education may not even be aware that it does not have to be that way.