You have two main options:
Option 1: Rename your data directory to _data.
Jekyll ignores files and directories that start with an underscore. You could also create a top-level _backend directory and then move your data directory into that.
Option 2: Configure your Jekyll to exclude the data directory.
You can add an exclude setting to _config.yml to tell Jekyll to ignore your data directory.
From the configuration documentation:
Exclude
Exclude directories and/or files from the conversion. These exclusions
are relative to the site's source directory and cannot be outside the
source directory.
exclude: [DIR, FILE, ...]
Googling "jekyll underscore directory" returns a ton of results, including this one which explains all of the above: https://help.github.com/articles/files-that-start-with-an-underscore-are-missing/