If you are trying to apply a Document Layout with Headers/Footers, you will be unable to use content files that employ Sections Breaks. TariffShark and MS Word require that a file be a single section in order to apply Headers/Footers.
Your two options are
1) change out any Section Breaks with Page Breaks which are Document Layout-friendly. However, this can often change your formatting and document flow. So be careful here.
2) Do not apply Document Layouts....if have already built content, the Build Content command will offer you Option 7 whereby you can change the Document Layouts of the TRV. Selected "X" will remove a Document Layout. This is always the safest option.