Q:

three.js filling gaps between edges

I created a model in Blender of a block with a hole in it:

I export it as an .obj file, and import it in ThreeJS with the OBJLoader add-on.
When I use it in my app, it appears to draw a face over the sides of the hole:

Is there a setting I need to use in ThreeJS to avoid having it close over gaps like this? Or is the problem in how I'm creating the model? I'm totally lost here, any guidance appreciated.
EDIT: I discovered through trial-and-error that the problem is having irregularly-shaped faces, like the ones adjacent to the hole. I "solved" my problem by triangulating the model; while this changes its shape slightly, it ensures that every vertex in the hole is part of a triangle face, which seems to be the magic answer.
I'm still very curious about why this is, especially since the triangulation has made the corners of the box a bit weird.
EDIT 2: Sorry for the delay. Here's the blender file: https://gofile.io/?c=EoxH1r

A:

The problem you are having is because of ngons (polygons with more than 4 sides).  
Modelling for three.js is just like modelling for games, so it is best to avoid polygons with more than 4 sides because when the renderer (or video card, I dunno) tries to render the model, it has to apply triangulation and may do it in an unexpected way.  
As you said, applying triangulation to the model fixed the issue, but automatically applying triangulation in your modelling app may also yield unexpected results. So your best bet is to alter the model so you get the results you expect.
Here is a youtube video I found that seems to explain a lot about ngons.
https://www.youtube.com/watch?v=BjnCV2PIkKA
(though I only watched the first minute or so)
Here is an example of how I would do it, red lines representing added edges. Remember to do it all the way around on both sides and apply your smoothing groups before exporting.

