I don’t think I’d seen Secret Origins since it premiered back in 2001 and since I was 11 at the time, there’s a lot I didn’t think about.

1. I’m not sure how old Diana is supposed to be when she decides to leave Themyscira, but she sounds like a teenager.
2. It’s never explained how much time takes place between JL and the previous DCAU series, but it was apparently long enough for Clark to meet John, even though Kyle was the first GL he’d met and the only one he was aware of, Wally to have met Bruce at some point, and the world to regain (for the most part) trust in Superman after then events of Legacy
3. (Most important point) Almost every member of the League kills one or more of the invaders. Bruce discovers that they’re incredibly vulnerable to UV light and the League promptly creates as many openings as possible to expose the invaders to sunlight. Clark cuts out a portion of the wall, crushing one and vaporizing the other two with sun, Bruce uses explosive batarangs the entire episode, Shayera and Diana smash them against walls, Wally and John wreck a few tripods (pretty much all of the invader tech seems to be organic, if not completely alive). This isn’t only inconsistent with the rest of the series, but with the characters themselves.
4. Bruce mentions that the Watchtower was paid for through funds “hidden in a line in the Aerospace R&D budget.” We see that Wayne Industries has worked in space travel in the Superman episode “Knight Time” but, at the time, they were only working on robots for exploring the surfaces of various planets and the project doesn’t seem to go anywhere, considering that astronauts are seen on Mars at the beginning of Secret Origins. How much money is Wayne Industries working with that he didn’t even have to go through another company to hide a SPACE STATION AND MULTIPLE SPACESHIPS in the budget? And does Wayne Industries continue to fund the expanded League of JLU, including  paying the dozens of human staff members?