I know that feeling -- I have a Fitbit, and when I play a long soccer game without it on, it feels like the steps and miles I ran "don't count." Which is silly. By the way, have you tried RunKeeper? The running app? I wonder how the two compare, Endomondo and RunKeeper.
In those cases I usually manually add the workout. It might have also been OxygenOS's fault, because after the workout crashed I couldn't turn the screen on for a while. When I rebooted my battery jumped from 21% to 8% to 3% in a few seconds. Luckily it stayed there for the rest of the run. When I last tried it I didn't find RunKeeper to be much better. Endomondo is also very good at taking all kinds of sports and activities and dealing with it. It works out of the box with my HR monitor and during the run I can easily check the map to adjust my route. I'll take the few times it shits itself if the rest of the time I get exactly what I want out of my running experience. Maybe when I'm more serious about a detailed tracking I'll give it a try.