Are you saying that the Excel file only refers to the DLL that you include in your project? This is a secondary link, and ClickOnce will not see it and will automatically include the file.
First, in your DLL, I assume that it refers directly to your project. If so, then make sure you add it to your project, and set "Build Actions" to "none" and "Copy to output directory" so that "not copy". Then remove the link to it and add it, pointing it to the version included in your project. Set the copy local property to true. This will ensure proper dll deployment.
For an Excel file, you will need to add it to your project. Set the build action to "content" and set "copy to output directory" to "copy always". It will not be included automatically, as it is a secondary link to the ClickOnce application, and not a direct / primary link such as a DLL.
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