For those of you who are curious/confused/frustrated, Nick was kind enough to explain why this is happening. Turns out those pets were never really that rare to begin with! The rarities were just inflated by a surge of spam accounts, and are now settling back into their true values.
Nick wrote:The only real way for the rarity of pets to fall is for the number of "active players" to drop, since this is used to work out how many people are competing to collect pets. That's the number of accounts that have logged in within the last year. In 2013, we had a huge number of accounts sign up and then not do anything in May, June and July (possibly caused by spambots, about 2-3x as many as normal). So when the rarities were updated in the last couple of months, the number of new people who had joined the site in those months this year was about 50% less than the number of accounts that had gone inactive in those months in the previous year, so the count of the number of "active players" over the past 12 months fell for three months in a row. This meant that the "rarity" displayed on all pets fell slightly in those months.