The issue seems to be an unannounced event that takes place where most of my fleet is decimated to the point of losing cruisers, capitals, and almost all fighters, as well as crew as if these ships took part in an autoresolve combat event when none has taken place.
This seems to happen when your fleet is directly on top of another fleet. The first time this has happened was when I just defeated a small fleet and had a few seconds of immunity of being intercepted. The proximity of the small fleet I intercepted was quite close to these two large fleets, so much so that after defeating them, my fleet was in the middle of theirs while the immunity thing was taking place. I shortly got out before the immunity worn out, and I believe being stuck inside of these two fleets resulted in the event where the AI autoresolved the battle in which no damage was attributed to the enemy fleet in question and my own fleet was quietly decimated without my notice.
I first found out that my fleet was in tatters was when I intercepted a small fleet soon after dodging out of the two big ones. Only one of my destroyers was operable, the rest having been destroyed, under crewed due to the rapid series of autoresolves, or just reduced to such a state that putting them into the line of fire isn't a good idea.
Edit: At first I thought it was just a lapse of judgement on my part, maybe I had pressed autoresolve without remembering it. This doesn't seem to be the case though as this happened twice, and now three times with what I can describe as a small fleet of a lowly frigate and a wing of interceptors reducing my own tier four fleet to tatters.