I believe they are in the Christian canon... why not Jewish?
As part of the Apocrypha, it's part of the Bible for Catholics, not Protestants.
The simple answer is that Judaism regards the Age of Prophecy as having ended about 2400 years ago, with Israel as a vassal state of Persia -- long before the Chanukah story. Anything after this point was no longer "Divinely inspired" (ruach hakodesh) like the earlier books, and therefore not Bible. (Though still possibly worthwhile, meaningful, valid, and/or wise.)
Professor Leiman suggests that the Tanach ends about 2400 years ago; the Christian New Testament suddenly picks up several centuries later. Hey, what about the time in between?! The Apocrypha conveniently fills in that gap. Further reason why the rabbis wanted that demarcation.
He also adds that a book could be written out if its ideas were contrary to Judaic belief or practice. (The book of Susana involves a.) Judaic courts administering the death penalty while under Babylonian rule b.) the punishment for "eidim zom'min" when the two witnesses conflict with one another.)
Maccabees' problem is most likely timing (and thus Divine inspiration, or lack thereof) and not content, to the best of my knowledge. There is some discussion about the war's precise Halachic status (milchemet mitzva vs milchemet reshut; yachid vs rabim), based on how it's described in Macabees.
While the focus of the Talmudic recounting of Chanukah is different from that of the Book of Maccabees, but that doesn't mean that the two conflict. Just a matter of what elements are emphasized.