For something with any interface you want, a tool being used incorrectly is a flaw in the tool itself. Unless you're going way out of your way to use it incorrectly.
That's a bit too broad. Someone holds a screwdriver incorrectly when screwing in a screw. The screw is slightly crooked because of the improper technique. Is the screwdriver fundamentally flawed because it allows the wielder to mess up? It's difficult for me to conceive something as portable, usable, cheap, and effective as the screwdriver, that does the same thing, and does not allow me to mess up. You have to make a sacrifice in some important category to get that. Programming languages can be pretty similar. Some are designed to make it harder to shoot yourself in the foot, but are far less popular (ADA is the example I'd use).
For a convincing (to me) argument against Powerpoint as the problem itself in poor presentations, see Edward Tufte's booklet/essay: http://www.edwardtufte.com/tufte/books_pp
