UA's IT department is a real mess. You are a victim of that. You received an overall poor experience, without question. I would be disappointed as well.
The folks with the "free upgrade" to E+, maybe they were assigned those seat because E- was full? Then you get into E+ for free if you don't select a seat on your original reservation.
Though, a few years ago when I had no status, I did receive a complimentary E+ seat on a flight to OGG from SFO, even though the flight wasn't full. I was happy about it, and have no real explanation.