The vowel after the g is an i
schwaEmarginate has one stressed syllable, MAR, and four unstressed ones. Those four vowels are all reduced in speech and all guessable in writing.
heard asemarganate
spelledemarginate
saidee-MAR-jin-ut
emarginate.
There is a whole small family here and all of it keeps the i: margin, marginal, marginate, emarginate. Marginate is a term in its own right, used of a leaf with a distinct rim, so the two words sit side by side in the same keys and differ only by the prefix.
Nearby in the file
emargenate emarginat emerginate emarrginate emarginute emarjinate
The rest are on the word page. All 11 spellings of emarginate.