A lack of adequate planning - which may have its roots early on in a pilots training.
How many schools are under financial pressure to increase throughput, and instructors under the same pressure (only get paid when they fly). Ground exams are more and more being left on a "teach yourself" basis. Now - people may have passed the exam, but be honest. how many learnt the subject, and how many have learnt to pass the exam?
Aviation, Airspace, ATC and Aircraft equipment are organic - always changing. You have to keep up with it all to stand a chance of not falling into the traps that are out there.
There are a few simple solutions. Don't just look at a chart - learn how to READ it (the two are different). When you plot the route fly the trip in your head beforehand - if you see a possible problem at that point think about how it could be averted.
If you have a GPS - LEARN how it ALL works, don't just press the "Direct" button.
If you have a VOR, NDB or DME in the aircraft same again - LEARN how to use it. How many people here have thought how they can fix their position just by using DME in an emergency (go on - think about it - the answer's relatively easy).
In short -people need to think out of the box, not inside the one that your PPL groundschool kept you in.
What is needed in addition is some form of mentoring sytem, where the experienced AND knowledgable (the two don't necessarily go together - believe me!) can talk things through face to face with people and have things demonstrated to them. Forums are great - but they lack that "one to one" that is often required to expand someone's knowledge.