Is factoid an Auto-antonym?

The answer is no, it is not a Janus word. The reason is simply that its two accepted meanings are not antonymous at all.

As for those meanings and their accepted usage, the American Heritage usage panel says this:

The suffix -oid normally means "resembling, having the appearance of." Thus, factoid originally referred to a claim that appears reliable or accurate, often because it has been repeated so frequently that people assume it is true. The word still has this meaning for many writers and readers; in our 2013 survey, 59 percent of the Usage Panel accepted it in the sentence The editorial writer relied on numerous factoids that have long been discredited. But factoid is also often used to mean a brief, somewhat interesting fact, and this sense has become common in recent decades. Some 64 percent of the Panel accepted this usage in the sentence Each issue of the magazine begins with a list of factoids, like how many pounds of hamburger were consumed in Texas last month. As the ballot results indicate, neither usage is overwhelmingly approved. If you use the word factoid, be sure the sentence makes it clear whether you are referring to a spurious claim, on the one hand, or an isolated, trivial, or mildly intriguing fact, on the other.

And as for the term's etymology, Farlex says this:

Coined by the novelist Norman Mailer from fact + -oid (as in android, humanoid), in reference to his fictionalized biography of Marilyn Monroe.