This is not an issue, actually It's fine.
Eclipse displays the package view (as you pointed in the first red
square) and also the directories inside your project (the second
As you can see in your screenshot, the first 3 folders contain the
package icon (that's because you are using the Package
Explorer view), then below your Maven dependencies you can find
the physical folders.
If you don't want to see your package folder you may consider using
Navigator view instead of Package
Btw, you can configure filters for your view by using:
Then select the filter you consider appropiated.