I had this. Basically, if you have two authors with the same surname some 'styles' e.g. APA format like to put in the initials of the person that is repeated e.g. if you have D.P thomas, and W.H Thomas, then endnote will put the initials so it is clear which one you are talking about. - even if you only reference one of them in your document.
However, if you have the same author, but it is cited differently in your endnote database e.g. D.P Thomas, D. Thomas, D.P.M Thomas, then endnote will think they are differetn authors, when in fact they are just put differently depending on the journal/authors preference. To combat this, you can 'copy' the authors name and then 'paste' it into any other reference that is by the same person - to ensure they all match up. E.g. so they all say D.P. Thomas. (if they are by the same bloke).
Failing that, it could just be how your style output is set. You can edit your style output in one of the menus - and you can tell endnote how you want references cited.