Of around 53,000 regular rated results since 1/1/2008, only about 750 involved players who played in more than one section of an event with the same starting and ending dates, or about 1.4% of the results. (There were 193 event IDs in which there were multiple sections with the same start and end dates with some players in more than one of those sections.)
In some cases these will have been ‘extra game’ sections.
If it turns out that WinTD and SwisSys don’t have sufficient capabilities for TDs to easily get the sections numbered in the order in which they should be rated I suppose we could add some kind of ‘rating sequence’ field, but that’s a non-trivial change both from the standpoint of the ratings programming/database and for TDs to utilize.
Besides extra games you may also see cross-sectional pairings (of players getting byes) with the game being including in the section of the winner.
The easiest way to get the sections sequenced properly in WinTD is to create them in the sequence you want them to be rated.
If you have a particular reason for rating them in a different sequence from how you created them then you can always create new sections in the sequence you want them to be rated and then use the merge function to move each old out-of-sequence section to its corresponding new in-sequence section. You can then delete the original sections (players and games will be in the new ones) and then everything can get rated in the sequence you want.