Not using a system properly?

Can a user not use a system properly?

I can see how they might not use it as it was intended or designed, but properly?

Assuming that properly means the same a correctly. (http://www.google.co.uk/search?q=define%3A+properly)
If a system can be used in a way other than a correct one, doesn't that mean that the program is at best flawed or, at worst, contains errors?

I suspect that this phrase ("not using it properly") is typically used when they mean not as intended.  If that is the case it means that the program is unnecessarily complicated. Doesn't it?