Can duplicate pg_hba entries result in a connection error?
No. Duplicate entries are basically ignored.

The documentation of pg_hba.conf describes how the rules work pretty well:


  The first record with a matching connection type, client
  address, requested database, and user name is used to perform
  authentication. There is no "fall-through" or "backup": if one record
  is chosen and the authentication fails, subsequent records are not
  considered. If no record matches, access is denied.


So the second and any subsequent duplicates will never be considered.
So duplicate entires can not be the cause of your error.