You need to examine the source HTML file. Odds are you will find the same references in that file (or files). And that means you have managed to overwrite your source with output files. The process of generating WebHelp adds these references.
Should the source HTML files contain any of those <?rh-placeholder elements or do those get added automatically by generating the WebHelp?
Rick may be training so I'll pop in.
I don't think Rick is saying all the items should not appear, rather that some should not and others should not be duplicated. I think Rick is saying that some should not appear (the WH stuff) and the others should not be duplicated. The likely reason is, as stated, that you have imported an output file so Rh has them from both when you created the output and now that you are generating again.
When you open the source topics in your project, are you seeing red squares appearing? If you are then that further supports Rick's theory.
Perhaps this link to Rick's site will help.
See www.grainge.org for RoboHelp and Authoring tips