Example: Ragnaros exist in The Firelands and The Molten Core raids. Defeating either will make Rarity consider both as defeated if they were to be used.

In practice, this isn't a huge problem because few bosses have been reused like that, and no known conflicts exist where both would be of interest to collectors.
t is, however, somewhat inaccurate when defeating one boss that exists in multiple difficulties (and can drop a mount on each) will automatically mark all difficulties as defeated. This would apply to the Antoran Charhound and G.M.O.D. mounts, as well as the one from Tomb of Sargeras and the Nighthold, presumably (not sure).

Since these bosses are fairly recent additions, it would be another expansion or so until most users will even notice it, but if there's a way to fix this that'd be preferable.

PS: It's a Known Issue, but it is worth revisiting to see if perhaps Blizzard added some ways this could now be resolved. This ties well into the lockout details being stored: In addition to the encounter name, the instance name (or something similarly unique) could be stored IF it is available via the API now.

FAQ:

Can Rarity show more than two items at once in the progress bar?Not at this time. There are now a few places where 3 or more items can be farmed at once, so I might add it at some point.

Obviously this should be removed after the issue is resolved.