The Variations feature uses one specific list to link items in the different labels together: the Relationships List.
The caveat is that as soon as an inconsistency exists in this list Variations will no longer work correctly. The problems that can occur can vary. Sometimes it is no longer possible to create a new variation for a page in a label. Sometimes the autospawn feature will fail to create variations of new sites.
As soon as you have a certain amount of sites and pages in your variation system this list becomes more or less unmanagable through the UI as everything is stored in this list in a flat format without folders.
In the past I have worked on several support cases where customers reported issue with Variations which ended up as inconsistencies in the Relationsships List.
Long awaited and finally shipped in SP2 is now a new STSADM command which allows to analyze and fix the Relationships List:
stsadm -o variationsfixuptool
-url <source variation site URL>
The granularity of what can be done is pretty good. E.g. it is possible to fix issues just for one specific site in the source variation label. Or for a specific site and all it's subsites.
You can find more details about this tool and all it's parameters in the following Technet article: