Sad to announce that this same colony swarmed yesterday.
Being a fairly new beekeeper, it was first in my life to witness a cloud of bees over the house, so it was amazing to witness such an event, but am devastated that I did not do anything to prevent the over-crowding.
What adds insult to injury is that the swarm landed on a tree close to the apiary, and I boxed it successfully without a single bee remaining on the branch (though there were a few hovering even after I sprayed the branch with honey bee robber liquid - btw, is it dangerous to inhale some of the vapors if the slight wind blows your way?), and when I opened the box a few hours later, they were all gone - every single one of them. Bummer.
First.. stop feeling so bad.
With everything thats going against those bees in this day and age, from Trachial and Varoa mites, to all of the diseases, chalk brood, sac brood, afb, efb, and CCD... whatever causes that... Insecticides, pesticeds, herbicides and the stuff that is smeared into the hives to control the mites, and then all of those things combining in the wax to cause further problems...
Well buddy, if your hive swarmed it was because you did something right. So stop kicking yourself.
Many times your going ot have a swarm no matter how hard you work to avoid it.
I run small upper entrances on my hives year round, in addition to the lower entrance, and that looked pretty normal for a decent hive.
Those bees had scouts out, and apparently they found a location they liked better than your box and headed out for greener pastures.