Two n's before the ending?
stress-doubleDoubling a consonant is how English marks a short stressed vowel. The stressed vowel in emarginate is followed by an r, and nothing else in the word is stressed at all.
heard asemarginnate
spelledemarginate
saidee-MAR-jin-ut
One n: emarginate.
Doubling has landed at the very end of a five-syllable word, four syllables past the stress, where nothing is emphatic enough to justify it.
Nearby in the file
emargenate emarginat emerginate emarrginate emarginute emarjinate
The rest are on the word page. All 11 spellings of emarginate.