The formatting of the bibliography (i.e. justification, indentation, spacing etc.) is managed by Word itself, not by the citation style. Word uses the so-called ‘formatting styles’ for this purpose (e.g. Heading, Normal, Title etc.). Sometimes it can happen that everything gets out of place. The easiest way to undo this is to change the citation style once (e.g. APA or IEEE) and then switch back to the desired style. This will more or less reset the formatting stzle and usually helps.