This can happen when using a citation style that imports MEDLINE journal abbreviations and overrides local Zotero citation information.
When choosing a citation style for a document, in the Zotero Document Preferences window, make sure that "Use MEDLINE journal abbreviations" is UNchecked.
Also, make sure that the Journal Abbreviation field for the citation is filled in if you are using a style that requires abbreviated journal titles -- otherwise, the bibliography will default to using the full journal title name.