It seemed to have visibility into the folder where season 2 is stored earlier:
Mar 25, 2020 18:27:17.953 [0x7fe5f0567700] INFO - Library section 2 (TV Shows) will be updated because of a change in '"/volume1/video/TV/Fleabag/Season 02"/Fleabag - S2E06 - Episode 6 WEBDL-2160p.mkv'
At least it did for that particular file. I don’t see any similar notifications for other episodes from that season, if they are present. Also, the naming is slightly off; that should be “S02E06” in there. Your season 1 stuff seems to have it right:
Mar 25, 2020 18:34:31.256 [0x7fe5f0567700] DEBUG - [Notify] Now watching "/volume1/video/TV/Fleabag/Season 01/@eaDir/Fleabag - S01E03 - Episode 3 WEBDL-2160p.mkv"
I’m not certain that small an inconsistency would throw off the matching logic, but that’s all I see immediately. Also, that appears to be for an earlier scan. For the most recent one, it doesn’t look as though the scanner sees anything under Season 02:
Mar 25, 2020 20:24:05.831 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:05.831 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:06.227 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:06.227 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:06.422 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:06.422 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:06.601 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:06.601 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:06.673 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:06.673 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:06.697 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 02
Mar 25, 2020 20:24:06.697 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 02
Mar 25, 2020 20:24:07.086 [0x7f1da3513740] DEBUG - Scanner: Processing directory /volume1/video/TV/Fleabag/Season 02 (parent: yes)
Mar 25, 2020 20:24:07.089 [0x7f1da3513740] DEBUG - Skipping over directory 'Fleabag/Season 02', as nothing has changed; removing 0 media items from map.
I’d expect it to look more like Season 01:
Mar 25, 2020 20:24:05.765 [0x7f1da3513740] DEBUG - Scanner: Processing directory /volume1/video/TV/Fleabag/Season 01 (parent: yes)
Mar 25, 2020 20:24:05.799 [0x7f1da3513740] DEBUG - Looking for path match for [/volume1/video/TV/Fleabag/Season 01/Fleabag - S01E01 - Episode 1 WEBDL-2160p.mkv]
Mar 25, 2020 20:24:05.832 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 01
Mar 25, 2020 20:24:05.832 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 01
Mar 25, 2020 20:24:06.224 [0x7f1da3513740] DEBUG - Looking for path match for [/volume1/video/TV/Fleabag/Season 01/Fleabag - S01E02 - Episode 2 WEBDL-2160p.mkv]
Mar 25, 2020 20:24:06.228 [0x7f1da3513740] DEBUG - -> Searching down into Fleabag/Season 01
Mar 25, 2020 20:24:06.228 [0x7f1da3513740] DEBUG - Checking descendants of Fleabag/Season 01
Can you show a screenshot of what the Add Folders looks like if you edit your TV library, and navigate all the way down to Fleabag season 2? Similar to the below:

(Don’t actually try to add that folder, you should only add the top-level TV folder. I just want to see if Plex can see the files within)