For example,
from folder \Series\Game of Thrones\Season 4\
There are files named
Game.of.Thrones.S04E01.Two.Swords.HD.TV-killers.mkv
Game.of.Thrones.S04E02.The.Lion.and.the.Rose.HD.TV-killers.mkv
Game.of.Thrones.S04E03.Breaker.of.Chains.HD.TV-killers.mkv
...
Game.of.Thrones.S04E08.The.Mountain.and.the.Viper.HD.TV-killers.mkv
Alongside these files there are subtitle files, like
Game.of.Thrones.S04E01.Two.Swords.HD.TV-killers.srt
Game.of.Thrones.S04E02.The.Lion.and.the.Rose.HD.TV-killers.srt
Game.of.Thrones.S04E03.Breaker.of.Chains.HD.TV-killers.srt
...
Game.of.Thrones.S04E08.The.Mountain.and.the.Viper.HD.TV-killers.srt
When I select the latest episode, MC always selects the first (in this case S04E01) subtitle file. When I go to subtitles, MC shows all the .srt files in that folder.
In the past, MC automatically selected the correct file corresponding to the s04e01 naming scheme but it stopped doing that for some reason.
Also, I think MC never showed files other then the ones matching the season/episode naming scheme but I'm not sure.
Game of Thrones is just an example, its happening for me with all my series, they are all named similarly though.