Or is it only the CS departments? Most write unmaintainable sphagetti code without any sense of proper data structures and the operations on them. Whenever a new functionality is to be added to their code, their code just crumbles and they have to rewrite everything. I have observed this many times.
The reason seems so obvious I interpret your question as a gripe rather than a sincere search for an answer. Anyone fresh out of school only has whatever they learned in school to work from. They won't have the experience that eventually leads at least some programmers to skills and effectiveness. Programming, like any complex skill, takes years of practice to master, along with aptitude and desire to get better. It stands to reason many people fresh out of school have just started down that path.
Same way a physicist specializing in electro-dynamics can't be expected to be a pro at designing PCBs for your electronic device.
CS should fundamentally taught bottom up, from basic microprocessors all the way to javascript. Once you have the fundamentals down, everything else on top is easy to integrate.