It tries to convey that one's work is necessarily dependent on the work of others and you can't treat your job as if you were in a vacuum, i.e. working in your own little bubble, independently of everyone else around you.
To exist in a vacuum = to be unconnected with other events
the program ensures that students understand that their work doesn't exist in a vacuum. = the program ensures that students understand that their work is connected with [something that has already been described, for example, other parts of the course and reality.]