Looks like most of the weapon bugs have been fixed with the patch today, and all saves seem to be okay. There are still a few minor bugs that have been reported and confirmed though.
* The Penetrator customization and upgrades no longer work. The menus are just blank.
* The Rectifier can no longer be customized
* There are duplicate dubstep guns now in weapon cache. The new duplicate seems to be from the mission that you use it, and is not customizable. The original one is still customizable and works correctly.
Minimaul was able to fix the penetrator and rectifier customization issues and you can download a temporary fix here.