That's what testing is for. When you note recurring incidence of testers getting stumped in the same spot, despite varying skill levels, you know the problem is in the layout/structure. That's when you have to identify if it's just too challenging a puzzle, an instructional oversight, or a technical bug.
EDIT:
But yes, I do agree, some games just do too much hand-holding.
One recent game I felt did it right was Guacamelee. It teaches you the basics early on then let's you off on your to experiment by combining abilities and using your skill to maneuvre around levels. Hints pop up when you've been around an area far too long, and even then they're relatively general hints like "press SELECT to find your objective" it doesn't drag you around by the nose.