I can't add an user/onboardee as it says that it already exists however I can't find her/him in the user list. What can I do?

That is probably happening because some filter category was left empty.

You have to be a super admin to perform the following. If not, contact the super admin of your company and ask her/him to perform it:

1. When in the onboardees' page, select "no filters" in the filter box:

2. You should be able to find the email;

3. Go to actions -> edit;

4. Check the filters and add the ones missing.