Have a lookover your site, it seems you have a reasonably advanced tag system set up.
When I’ve come across these issues before it is often a parent/child tag relationship that’s auto-adding the extra ones on (a child tag can’t exist without a parent one, so one will often be auto-added to ensure consistency). Depending on how you’ve structured everything, this can sometimes lead to unexpected behaviour.
Are you using parent/child tags at all for your tagging system?