I have the same problem but trying to configure a simple cronhob with Whenever Gem, here is the error:
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:80:in pwd': Operation not permitted - getcwd (Errno::EPERM) from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:80:in lockfile_contents'
from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:68:in lockfile_version' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:22:in bundler_version_with_reason'
from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:7:in bundler_version' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/bundler_version_finder.rb:45:in filter!'
from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems/dependency.rb:284:in matching_specs' from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems.rb:272:in find_spec_for_exe'
from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/rubygems.rb:302:in activate_bin_path' from /usr/bin/bundle:23:in '
Do you have any idea?