In the upcoming WordPress 4.2 release, whenever a shared term is updated it will be split into separate terms. If you are running any plugins or themes that store term IDs they may change after being split, which can cause data integrity issues. You can find an in-depth explanation and guide for how to update your code over at the Make WordPress Core blog.
It’s not easy to tell at a glance whether this issue will affect your site, so I’ve built a small plugin, Find Shared Terms that will detect any shared terms in your WordPress install and list them along with the taxonomies they belong to. This may be helpful in determining whether you need to refactor any custom code that stores term IDs or upgrade any of your plugins prior to the 4.2 upgrade. If your site doesn’t have any shared terms, and you’ve already upgraded to 4.1 then you’re in the clear!
If the plugin does detect shared terms, it doesn’t necessarily mean you’ll have an issue, but you’ll want to review any custom code you’ve written to check for anything that’s storing term IDs and check your list of plugins against the plugins listed in the Make post.
Pull Requests are welcome on Github.