Well, I suppose one discrepancy could be the appearance of the Daily Planet building. Presumably the interior was rebuilt after the Joker attack (I think they redressed the CatCo sets), but did the exterior, or the cityscape beyond, look anything like the one from SR? Well, any difference could be chalked up to artistic license and available digital assets.
I adored the production design of the Daily Planet in Returns, and examined it pretty closely a couple years ago as inspiration/reference for a project I did, so I was on the lookout for how this version of the bullpen would come out. I was pleasantly surprised by how many little touches the TV team put in to evoke it; I wasn't expecting anything except for the framed front pages based on the publicity shots, but they did put in a number of smaller touches, as well. The elevators had the brass doors (though was missing the elaborate inlays and reliefs) and black marble frames, and the waist-high marble trim. The general layout is also pretty similar. Personally, I'd head-canon that they moved to a different floor than the office in the movie after the Joker's attack, one that had been through one of those awful remodels where they cover up all the period detailing with plain white drywall and cheap fixtures. The next tenant is probably going to take up the linoleum and find beautiful marble floor tiles, just like all those stories of people ripping up shag carpets from the '70s and finding hardwood that would cost a fortune to put in today.
The city was totally different, more modern-looking glass and metal than the brownish Australian backdrops of the film, and was an entirely CG field of instanced generic skyscrapers. The building itself was similar to the film (looked like vintage '30s, and terraced up to a point), but smaller than in the movie, maybe half the size (it was represented by a model in the film; based on the way we mostly see the whole building from one angle, I suspect the main street-level shot was a paint-over of a photo of a real building, with the full building model seen in the distance not being made to close-up standards. The distant building was also slightly cockeyed from the street grid, for some reason). The globe was pretty different as well but, then, the globe was destroyed in the film, so maybe they just got an uglier replacement.
All in all, I expected something really generic considering how little we'd see of this version of the Planet and how much else would be going on in the crossover; the redress of the elevators, while not a major effort, does let me know that they popped in the DVD and looked through the archives to see how much they could recreate with what they had on-hand.
(It's funny, I was just talking a few days ago about official projects using cutting corners and stealing fan-art, but, honestly, if someone had told me we'd be getting a Superman Returns continuation that could've used it, I absolutely would've done a 3D set and exterior recreation after the head-start I got with the other project I mentioned, and left it where it'd be easily googleable under a CC0 to help out the shows. I still might, they'll have to build a Daily Planet for the new Superman show.)
Also, having pulled up the episode and the movie and scrubbing through them, it's probably that it's just because there are only so many ways to film a man flying at speed, but the shot of SR-Superman initially charging reminds me of him rushing to catch the crashing plane in the movie, and SG-Superman in charging back reminded me of the first flight scene from Man of Steel. But, like I said, it's a pretty obvious angle, combined with the 180° rule and the fact that the two movie shots I mentioned were pretty prominent in the advertising, so they'd stick in my head.
Or Kevin Conroy, for that matter -- counting video games, this is approximately the 15th distinct version of Batman he's played. (The others are... Gotham Knight...)
Where, to add an extra dash of confusion, Conroy was playing Christian Bale's Batman.