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It seems as though, for at least a couple shows, TVDB scrapper is using either the DVD release number, or the "combined episode number," from the API to sort episodes. I exported my library to see what the issue is, and below is an example from Check It Out! with Dr. Steve Brule (http://thetvdb.com/?tab=series&id=163751):

Code:
<episodedetails>
            <title>Health</title>
            <showtitle>Check It Out! with Dr. Steve Brule</showtitle>
            <ratings>
                <rating name="default" max="10" default="true">
                    <value>7.000000</value>
                    <votes>2</votes>
                </rating>
            </ratings>
            <userrating>0</userrating>
            <top250>0</top250>
            <season>1</season>
            <episode>1</episode>
            <displayseason>-1</displayseason>
            <displayepisode>-1</displayepisode>
            <outline></outline>
            <plot>Dr. Steve discusses the topic of being ugly or pretty. A look at a high school quarterback. Also, spiritual health. Maria Bamford guest stars, and pornstar Ms. Deja appears in aerobics segment.</plot>
            <tagline></tagline>
            <runtime>11</runtime>
            <thumb>http://thetvdb.com/banners/episodes/163751/2339601.jpg</thumb>
            <mpaa>TV-MA</mpaa>
            <playcount>1</playcount>
            <lastplayed>2017-07-07</lastplayed>
            <file></file>
            <path>REMOVED/Check_It_Out_with_Dr_Steve_Brule/Season_01/</path>
            <filenameandpath>REMOVED/Check_It_Out_with_Dr_Steve_Brule/Season_01/S01E01.mp4</filenameandpath>
            <basepath>REMOVED/Check_It_Out_with_Dr_Steve_Brule/Season_01/S01E01.mp4</basepath>
            <id>2339601</id>
            <uniqueid type="unknown" default="true">2339601</uniqueid>
            <genre>Comedy</genre>
            <premiered>2010-05-16</premiered>
            <year>2010</year>
            <status></status>
            <code></code>
            <aired>2010-06-06</aired>
            <studio>Adult Swim</studio>
            <trailer></trailer>
            <fileinfo>
                <streamdetails>
                    <video>
                        <codec>h264</codec>
                        <aspect>1.772727</aspect>
                        <width>624</width>
                        <height>352</height>
                        <durationinseconds>664</durationinseconds>
                        <stereomode></stereomode>
                    </video>
                    <audio>
                        <codec>aac</codec>
                        <language>und</language>
                        <channels>2</channels>
                    </audio>
                </streamdetails>
            </fileinfo>
            <actor>
                <name>John C. Reilly</name>
                <role>Dr. Steve Brule</role>
                <order>0</order>
                <thumb>http://thetvdb.com/banners/actors/293389.jpg</thumb>
            </actor>
            <resume>
                <position>0.000000</position>
                <total>0.000000</total>
            </resume>
            <dateadded>2017-01-02 12:57:24</dateadded>
            <art>
                <thumb>http://thetvdb.com/banners/episodes/163751/2339601.jpg</thumb>
            </art>
        </episodedetails>

You can see the episode is labeled 1. Below is the same episode from the TVDB API:

Code:
<Episode>
  <id>2339601</id>
  <Combined_episodenumber>1.0</Combined_episodenumber>
  <Combined_season>1</Combined_season>
  <DVD_chapter></DVD_chapter>
  <DVD_discid></DVD_discid>
  <DVD_episodenumber>1.0</DVD_episodenumber>
  <DVD_season>1</DVD_season>
  <Director></Director>
  <EpImgFlag>2</EpImgFlag>
  <EpisodeName>Health</EpisodeName>
  <EpisodeNumber>4</EpisodeNumber>
  <FirstAired>2010-06-06</FirstAired>
  <GuestStars></GuestStars>
  <IMDB_ID></IMDB_ID>
  <Language>en</Language>
  <Overview>Dr. Steve discusses the topic of being ugly or pretty. A look at a high school quarterback. Also, spiritual health. Maria Bamford guest stars, and pornstar Ms. Deja appears in aerobics segment.</Overview>
  <ProductionCode></ProductionCode>
  <Rating>7.0</Rating>
  <RatingCount>2</RatingCount>
  <SeasonNumber>1</SeasonNumber>
  <Writer></Writer>
  <absolute_number>4</absolute_number>
  <filename>episodes/163751/2339601.jpg</filename>
  <is_movie>0</is_movie>
  <lastupdated>1355782034</lastupdated>
  <seasonid>248261</seasonid>
  <seriesid>163751</seriesid>
  <thumb_added></thumb_added>
  <thumb_height>225</thumb_height>
  <thumb_width>400</thumb_width>
</Episode>

The combined episode number and DVD episode number are both 1, but the absolute number and episode number are 4 (which is what I would expect). I'm guessing it's most likely using the Combined_episodenumber field, which doesn't appear to be something a standard user can edit on TVDB. It would be better if this used the episode number instead.
You haven't stated what you actually want to happen. How do you want them sorted?

Also...
1. How did you come about this error?
2. Was this show existing in your library, and you tried to add new episodes?
Moving to Metadata Add-ons
It wouldn't be the first time that the order of a TV series was different to a DVD release.
You can try make a request on the TVDB forum for a change, but those requests are not always successfull.
(2017-07-09, 08:01)Karellen Wrote: [ -> ]You haven't stated what you actually want to happen. How do you want them sorted?

Also...
1. How did you come about this error?
2. Was this show existing in your library, and you tried to add new episodes?

Sorry, thought I did. I'd like it to be sorted by the Episode number (or air date, really). I came across the error while playing the episode labeled "Health" and it played a different episode. The episode it's playing is the actual first episode, which is fine, I'd just like them to display correctly in KODI. I could probably just edit the NFO files but it seems like a lot of trouble to go through for this. This is happening to other shows in my collection, as well. I just haven't gone through to verify all of them.