Still have this issue. Looked like this was fixed in the newest release notes:
Updated to Plex Media Server 1.23.2.4625 on Ubuntu 18.04 LTS, and the issue persists after update and machine reboot. My directory structure is the same as above. I retested the same episode /media/plex_storage/ripped_media/TV Shows/The Office (US)/Specials/The Office (US) - s00e314 - Season 3 Ben Franklin Deleted Scenes.mp4. Season 1, Episode 1 played instead. Here is my XML data again (in case it changed) for this episode, as well as newly export PMS logs just following the test:
<MediaContainer size="1" allowSync="1" identifier="com.plexapp.plugins.library" librarySectionID="9" librarySectionTitle="Fisher TV Shows" librarySectionUUID="e12ea0fd-8ada-4efc-8442-d8722e374d19" mediaTagPrefix="/system/bundle/media/flags/" mediaTagVersion="1622556413">
<Video ratingKey="3409" key="/library/metadata/3409" parentRatingKey="3289" grandparentRatingKey="3288" guid="com.plexapp.agents.thetvdb://73244/0/314?lang=en" parentGuid="com.plexapp.agents.thetvdb://73244/0?lang=en" grandparentGuid="com.plexapp.agents.thetvdb://73244?lang=en" type="episode" title="S03E14 - Ben Franklin - Deleted Scenes" grandparentKey="/library/metadata/3288" parentKey="/library/metadata/3289" librarySectionTitle="Fisher TV Shows" librarySectionID="9" librarySectionKey="/library/sections/9" grandparentTitle="The Office (US)" parentTitle="Specials" contentRating="TV-14" summary="" index="314" parentIndex="0" thumb="/library/metadata/3409/thumb/1609030551" art="/library/metadata/3288/art/1620244234" parentThumb="/library/metadata/3289/thumb/1608927740" grandparentThumb="/library/metadata/3288/thumb/1620244234" grandparentArt="/library/metadata/3288/art/1620244234" grandparentTheme="/library/metadata/3288/theme/1620244234" duration="455727" addedAt="1609030520" updatedAt="1609030551">
<Media id="3416" duration="455727" bitrate="812" width="720" height="364" aspectRatio="1.78" audioChannels="2" audioCodec="aac" videoCodec="h264" videoResolution="sd" container="mp4" videoFrameRate="24p" optimizedForStreaming="0" audioProfile="lc" has64bitOffsets="0" videoProfile="main">
<Part accessible="1" exists="1" id="3447" key="/library/parts/3447/1609023662/file.mp4" duration="455727" file="/media/plex_storage/ripped_media/TV Shows/The Office (US)/Specials/The Office (US) - s00e314 - Season 3 Ben Franklin Deleted Scenes.mp4" size="46614526" audioProfile="lc" container="mp4" deepAnalysisVersion="4" has64bitOffsets="0" indexes="sd" optimizedForStreaming="0" requiredBandwidths="876,876,876,876,876,876,876,876" videoProfile="main">
<Stream id="6694" streamType="1" default="1" codec="h264" index="0" bitrate="638" anamorphic="1" bitDepth="8" chromaLocation="left" chromaSubsampling="4:2:0" codedHeight="368" codedWidth="720" colorPrimaries="smpte170m" colorRange="tv" colorSpace="smpte170m" colorTrc="bt709" frameRate="24.004" hasScalingMatrix="0" height="364" level="40" pixelAspectRatio="8:9" profile="main" refFrames="4" requiredBandwidths="703,703,703,703,703,703,703,703" streamIdentifier="1" width="720" displayTitle="SD (H.264)" extendedDisplayTitle="SD (H.264)"> </Stream>
<Stream id="6695" streamType="2" selected="1" default="1" codec="aac" index="1" channels="2" bitrate="160" language="English" languageCode="eng" audioChannelLayout="stereo" profile="lc" requiredBandwidths="159,159,159,159,159,159,159,159" samplingRate="48000" streamIdentifier="2" displayTitle="English (AAC Stereo)" extendedDisplayTitle="English (AAC Stereo)"> </Stream>
<Stream id="6696" streamType="3" default="1" codec="vobsub" index="2" bitrate="7" language="English" languageCode="eng" requiredBandwidths="8,8,8,8,8,8,8,8" streamIdentifier="3" displayTitle="English (VOBSUB)" extendedDisplayTitle="English (VOBSUB)"> </Stream>
<Stream id="6697" streamType="3" codec="vobsub" index="3" bitrate="7" language="Español" languageCode="spa" requiredBandwidths="8,8,8,8,8,8,8,8" streamIdentifier="4" displayTitle="Español (VOBSUB)" extendedDisplayTitle="Español (VOBSUB)"> </Stream>
</Part>
</Media>
<Field locked="1" name="title"/>
<Extras size="0"> </Extras>
<Related> </Related>
</Video>
</MediaContainer>
