No, plug-ins should never conflict or clash. You should have registered a four character prefix with Adobe. Then everything you register in a shared space (e.g. menu names, plug-in name, select server name, filesystem name...) must start with this prefix. You will probably see samples using ADBE; you MUST change this to your own prefix. Some Adobe samples won't use a prefix (e.g. SelectionServer): you must add one.
There remains the possibility of a UI clash (e.g. two plug-ins add identically named menus) but these will be distinct in the eyes of Acrobat.
