Merge Accounts will delete the "New User" and update the "Existing User" based on the differences noted. 
This error may occur if one of the users being merged has Course Requests or an Application. Additionally, a Candidate can only be merged with other Candidates, not Students

To determine why you are unable to merge duplicate users:
  1. Core > User/Access > Profile
  2. Edit User Profile Data
  3. Search the New User 
  4. Scroll Down to System Information
  5. Click Remove User
  6. Once Remove User is clicked it will provide the message and tell you why the User cannot be deleted. For example:"To permanently remove this student, all school registration rows must be deleted first. An alternative is to withdraw him/her and assign the Past Student role."