When people are referring to a "Rare Pepe" they are often referring to a Pepe that is not often seen or a newly created version of the classic frog meme. A number of people started asking questions when the Anti-Defamation League posted a very particular image of Pepe which was then featured as part of their coverage on the Pepe meme by CNN news.
What led people to believe this was a highly unusual image of Pepe is the fact that when you initially attempted to reverse image search it, you would find a complete lack of results, which led some internet users coming to some interesting conclusions and speculations about this Pepe's origin. It further became complicated with the fact that if you reverse image search it today, the origin point is shown to be the ADL.
So in an effort to figure out if it had an alternate origin some searching was required, and it took admittedly more time than you might think. The origin of this Pepe comes from a 7-month-old reddit post that refers to it as "Spooky Ghost Pepe". If you type in Spooky Ghost Pepe into a google search you will find it as the first image result.
It appears this particular Pepe image never become all that popular and was never really used much outside of the one reddit post and was then dug up by the ADL and used as an example of racist hate symbols that featured Pepe. It is certainly odd that an image that was initially this difficult to find would be cited as an example of such, but in the very least this rare pepe has had its origins discovered.