Background reading: #30335 and the notes on shared term splitting in https://make.wordpress.org/core/2014/11/20/dev-chat-summary-november-19th/.
As part of the work on the taxonomy roadmap in 4.1, shared terms (terms which are shared across more than one taxonomy due to a slug collision) now get split when the term gets updated. The end result being that editing a term in one taxonomy will no longer affect the term in another taxonomy.
Many plugins store term IDs in post meta, options, terms (!), etc, and the side effect of shared term splitting is that these caches can break when the ID of a term they reference changes. Not only that, but the breakage (and the cause) can be invisible to the user and hard to track down if they do notice it.
Following a discussion in #core Slack I’m proposing that shared term splitting is removed from 4.1 and we’ll add it back in for 4.2 and allow a full release cycle to get the word out to developers about the change. I’ll make the final decision during tomorrow’s dev chat.
Thanks in particular to @mboynes for his time spent on this.
(Note that this only affects existing terms; new terms do not get shared since r30240.)