Hi Tim. I think that looks pretty cool with the overlap! But for your purposes I THINK (but not 100% sure) its that your body div is specified to be 400px high. So your images are pushing over that division with the flex box. Its a bit difficult to see because when I look at the site I cannot see any pictures. Maybe just make it 100% and see what happens?
By the way someone pointed me towards cloudinary, a very nice place to put your pictures and stuff that is accessible for codepen.
I guess you can put the pictures in some bootstrap grids using the div row and div col tags. But I think that CCS images gallery I proposed earlier would look pretty cool with the site.
Another thing a friend pointed out to me: Inspect element. Not sure if you know this one. If you put your pen in full page view, right click and select inspect element. You can see the elements you used highlighted and it really helps me with layout problems.