First, a very old bug/feature:
https://core.trac.wordpress.org/ticket/5809

Currently, if you have WP Category for fruits called “Apple” and a WP Tag for pies called “Apple” and a custom taxonomy such as “Computer Manufacturers” with an item called “Apple”, that “Apple” term is shared between everything. This isn’t much of a problem until you decide to rename the computer manufacturer to “Apple Computers”, at which point you’ve also renamed the fruit and pie. For the past seven years the only solution to this has been to create a new term instead and manually re-tag everything.

Last year one of the core developers, Andrew Nacin, outlined a roadmap for fixing this, with the expected final change to land in 4.x somewhere in 2015
https://make.wordpress.org/core/2013/07/28/potential-roadmap-for-taxonomy-meta-and-post-relationships/

One part of this roadmap that was to land in 4.1 was when a shared term was detected by the system during an edit, the system would automatically break the share and create unique unrelated terms. So if you edit the Apple computer term in any way (or just hit save on it), WP would detect that it is used in multiple contexts and break that computer one away into a dedicated context of its own.

Sounds like a good plan except it turns out a lot of people having been storing/caching the underlying ID of the shared term instead of the term itself. So developers have been storing “term 48” instead of just “apple” since developers like numbers.

This is a pretty big potentially breaking change but was luckily rolled backed a couple of days ago:
https://core.trac.wordpress.org/changeset/30336

This was re-introduced and in theory fixed four days ago however I can still think of many edge cases that can break:
https://core.trac.wordpress.org/changeset/30344