I recommend moving both out completely, scanning files, empty trash, and clean bundles.
As the next step, if MP4 files, verify there is no embedded metadata which is ambiguous.
As demonstration, I created test MKV files and matching was correct.
[chuck@lizum mmg.86]$ ls -la /vie/qa/tv/Magnum*
/vie/qa/tv/Magnum, P.I. (1980):
total 64
drwxr-xr-x. 6 chuck chuck 4096 Jan 5 23:51 ./
drwxr-xr-x. 901 chuck chuck 45056 Jan 5 23:53 ../
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:51 Season 01/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:51 Season 02/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:51 Season 03/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:51 Season 04/
/vie/qa/tv/Magnum P.I. (2018):
total 64
drwxr-xr-x. 6 chuck chuck 4096 Jan 5 23:46 ./
drwxr-xr-x. 901 chuck chuck 45056 Jan 5 23:53 ../
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:46 Season 01/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:46 Season 02/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:46 Season 03/
drwxr-xr-x. 2 chuck chuck 4096 Jan 5 23:46 Season 04/
[chuck@lizum mmg.87]$ ls -la /vie/qa/tv/Magnum*/*01/*S01E01*
-rw-r--r--. 1 chuck chuck 286 Jan 5 23:51 /vie/qa/tv/Magnum, P.I. (1980)/Season 01/Magnum, P.I. (1980) - S01E01.mkv
-rw-r--r--. 1 chuck chuck 284 Jan 5 23:46 /vie/qa/tv/Magnum P.I. (2018)/Season 01/Magnum P.I. (2018) - S01E01.mkv
[chuck@lizum mmg.88]$
