I've attached a RStudio project that reproduces this error. Here is a brief summary:

_bookdown.yml has these two lines:

rmd_files: ["index.Rmd"]
rmd_subdir: ["chapters"]

There's also a file in the project's root directory, ./Notes.Rmd. Now, as I understand how the rmd lines above are supposed to work during a build is to read index.Rmd and then recursively include everything in ./chapters/. But the build results include the contents of ./_Notes.Rmd. They shouldn't.
BookdownTest.zip

This is my very first new issue on github. I didn't notice before, but the zip file of my reproducible example was added twice. I don't think this should be a problem, and I'm afraid of damaging the issue bundle by deleting it here. So it appears twice.

xfun::session_info()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6, RStudio 1.2.5042

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  base64enc_0.1.3 bookdown_0.18   compiler_4.0.0  digest_0.6.25   evaluate_0.14   glue_1.4.0     
  graphics_4.0.0  grDevices_4.0.0 highr_0.8       htmltools_0.4.0 jsonlite_1.6.1  knitr_1.28     
  magrittr_1.5    markdown_1.1    methods_4.0.0   mime_0.9        packrat_0.5.0   Rcpp_1.0.4.6   
  rlang_0.4.6     rmarkdown_2.1   stats_4.0.0     stringi_1.4.6   stringr_1.4.0   tinytex_0.22   
  tools_4.0.0     utils_4.0.0     xfun_0.13       yaml_2.2.1   

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  • If I have posted the same issue elsewhere, I have also mentioned it in this issue.
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  BookdownTest.zip

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BookdownTest.zip