First of all, as the title of this discussion says, episode 13 is not from the first season.

Second: If we went to the anime website we see that this episode is listed as the second season, this is also said in the synopsis itself.

ついに始まったアニメ第2期 (Literally translated: Season 2 has finally started!)

Link: https://hyakkano.com/story/season2

Trird: In the anime itself the characters talk about the second season.

Fourth: if we go to websites specialized in anime like Myanimelist, Anilist, Kitsu or Anidb. They all list 2 seasons.

Links: https://myanimelist.net/anime/57616 https://anilist.co/anime/172258 https://kitsu.app/anime/kimi-no-koto-ga-daidaidaidaidaisuki-na-100-nin-no-kanojo-2nd-season https://anidb.net/anime/18343

Anime should not be treated the same way as a television series, Regardless of whether the episode number is 13, it is from the second season.

Anime should be listed in the correct way.

I hope I managed to express what I wanted to say, my English is not very good, so at times I used Google Translate.