The door should close all the way when the Clip Director (green knob) is in the full
MULCH position.
Clippings and other debris can collect in and around the door and it's moving parts, sometimes preventing it from closing all the way.
Tip the mower on it's right side (air cleaner UP) and inspect under the deck. Often, a garden hose can clear away all the clippings, mud, etc. that can cause this problem. If everything is clear and clean, and the door still won't close, it's possible it's come out of alignment or some other adjustment. If this is deemed to be a factory defect (and not the result of damage or accident) then the repair would usually be covered under warranty. You can locate a servicing Honda dealer by using this link:
http://powerequipment.honda.com/dealer-locator
-Robert@Honda
Caveat: I work for Honda, but the preceding was my opinion alone.