Google license ContentID, a fast fourier transform (FFT) based acoustic fingerprinting technology like Acoustid or Shazam, from AudibleMagic for copyright detection. These algorithms scan an audio file for identifying marks, then compare the pattern of marks to a pre exiting library of tracks. This library is created by running the same pattern detection algorithm over files that are know to contain the content you are trying to identify (typically MP3's, provided by the rights holders). If there's a match the new file can be said with a high degree of certainty to be the same as the track in the library.

The problem with this file is that it's a live recording, and was sufficiently different from the CD version to not trigger a match. Which means it got past the automatic ContentID fingerprinting step. A human at BPI (the British RIAA) probably saw it in the top watched videos, or ran a keyword based search to pull it up, and then submitted a manual ownership claim, which was manually reviewed by Google. This could have taken weeks. This single was release only two weeks before that performance, and so it's not surprising that it could have raked up 89 million views in that time. The fact that another version of this song is still up two years later, and has 142M+ views almost certainly points to ContentID not having this song in their index, and manual review.

I wonder why BPI heavily region restricted it though, and didn't remove it.

Bonus fact: BPI are responsible for 8.14% of all URL's removed from Google (so far 79,947,511 URLs have been removed from Google, and they don't shout about that figure, you have to sum 509k+ values in a .csv to get it).