I just did a quick test with this naming and folder organization and it worked fine with the modern, default Plex TV Series scanner and Plex Series agent (the library points to “test_tv”):
test_tv/
└── 24 (2001)
└── Season 01
├── 24 (2001) - S01E01.mkv
└── 24 (2001) - S01E02.mkv
I’d double check that you’re closely following Plex’s TV series naming/organization guidelines for not only this series, but the others in your library as well. It could be that “24” is being added as duplicate episodes in another series. You should be able to view your library by episodes and then apply the “Duplicates” filter to see any duplicates. If that’s the case, you can correct any naming/organization issues and then Plex Dance the affected series to see if that straightens things out.