Perhaps you are observing the effects of property promotion/demotion.
If an Office file (or email or tiff file) is uploaded to SharePoint then SharePoint will insert additional metadata (e.g., Content Type) into the file. As a result the file in SharePoint will have slightly different metadata properties and will be slightly larger (order of a few kBs).
If you upload the same source file to exactly the same location in SharePoint then the resulting file in SharePoint should be identical.