To reproduce:

1. Get an endermite in a boat
2. press F3 and b to show hitboxes

       you can't see the hitbox of the endermite, only the hitbox of the boat.

       3. look to the bottom side of the boat ( best set it on transparent blocks)

        you can see the endermites hitbox coming a little bit below the boat one.

       4. Try to nam the endermite with a name tag.

        You can't name the endermite.