I had this issue due to symlinks: https://github.com/typescript-eslint/typescript-eslint/issues/2987

Opening the project directory via the true path rather than the symlink solved the problem for me.

# Compare these two outputs, if they are different than you are in a symlinked directory
pwd -P    # Shows the physical path (real path after resolving symlinks)
pwd -L    # Shows the logical path (path with symlinks)`

# Navigate to the non symlinked directory
cd $(pwd -P)