Some databases import only the abbreviated journal name while your style may call for the full journal name – and vice versa. Endnote provides a Journals Term List, so the journal names in your bibliography are either the full name or the abbreviation, as your style requires.
If the journal name in your actual imported reference doesn't match up exactly with the full name or one of the abbreviations in the terms list, the substitution will not take place.
A single space or the inclusion of a period at the end of the name is enough for it to not be considered a match.
If the journal name or abbreviation is incorrect in the reference--Go to the journal name field in the reference and correct it.
If the journal name or abbreviation is incorrect in the Journal Terms List-- Go to Tools > Open Terms List > Journals Term List> Select Journal > Edit Term