2 possible sources.
gobjects. so you have to delete them serverside in the database
effects added in noggit and noggit is not able to render them. use loadinfo and fileinfo to check the adts models if you find them. for test just delete all m2s on the adt and have a look if they are still there. keep in mind that if the bounding boxes hit adt borders you can habe them on more then one adt. cleare this by turn on the map and chunk lines in noggit.
for further help feel free to add me in skype. project. modcraft