Frameworks were sometimes used, although their effect on security is somewhat baffling at first sight -- and this is regardless of the platform, although we found most issues with PHP and J2EE. Sure, when you use the framework for security-critical things such as constructing SQL queries (SQLi) or HTML output (XSS), things work quite well. However, since most developers don't think about these issues, the single time they have to "escape" from the framework, since it doesn't (or they just think it doesn't) support a certain scenario, they don't know about all the things PHP and in smaller ways, J2EE requires to do for security.
Of course, this way, the framework protects 9x% of the application, but the asymmetry of security is that the attacker only needs a single vulnerability while the defender must patch it all.