I agree with what @nirgrahamuk says.
You can use the {git2r} package to perform git actions with a bit more control than the pane gives you, but without having to go down to the Command Line level.
You can use git2r::ls_tree() which will give you a data.frame with all the files in the most recent commit and you can check if your file is in there (search in the columns path and name for your file).
You can also run git2r::status() to see what files are in your git directory that have been modified/created but haven't yet been commited (this is essentially what is in the git pane).
You should also check the .gitignore file in your git directory as the file may have been put in there by accident. If it has, just remove it and it should re-appear