>To calculate the real dislikes on a video, we tabulate only increases to the dislikes, and ignore decreases. On normal YouTube videos (e.g., on PewDiePie's videos), the official YouTube stats and our real stats completely agree. On many White House videos, there is a huge discrepancy between official dislikes and our calculated real dislikes.

This might not be nefarious manipulation. YouTube may be removing illegitimate dislikes, such as from bots or sock-puppet accounts.

Some small amount is expected. For example, if it happens across samples, disliking and then changing it to a like would be counted. Or, like you suggest, if it's clear that it was done by a bot, it could be OK for Google to remove it, and it wouldn't be meaningful. But could that ever explain 95% of the downvotes being hidden?