There is definitelly something strange here. See where the box primitive is mirrored with a cylinder primitive mapped to its side: . Weird primitive mirror.JPG . I think since it is not a simple geometry but a primitive that needs attachment when created it has to take it from somewhere and takes it...
Why the Pad001/Pocket010 combo when this can be a simple Pad?
If you have mirored features better do them that way or use a single sketch to form them.
For the pocket you need separate noncrossing/nontouching loops for it to work properly.