Personally, I would say that don't believe the findings of these tools are rule written on rock. There are ways to configure the tools to tweak some rules. It's better to speak to some expert if you have iota of doubt.
In case of passing objects to method parameters instead of primitives, the reasons I can think of :
1. Java is considered as object oriented language. So deal with objects where-ever you can.
2. Passing primitives as object would give access to some more functionality related to object.
3. By passing objects, there is a scope of extending some functionality.
Of-course, the above objectives can also be achieved by passing primitive and converting to object inside method.