You've informed us that the latest patch (1.0.12) has brought one unexpected issue with functionality of controllers. We hear you and it's fixed. No longer do you need to jump and shoot at the same time.
However, if you need the urge to do jumping shots still, it's possible, of course - you'll just need to use two buttons at once ;)
- fixed a bug where controller's triggers would trigger both jumping and shooting at the same time.
Have a nice weekend!