Probably you've terminated update process, so some packages have been updated but older version haven't removed. If yum-complete-transaction really doesn't help (what the output by the way?) You may try to remove duplicates manually. Select older version of each package and run as root
rpm -e package1_name-version package2_name-version ... packageN_name-version
(putting version of older package into the command is important!)
Also you'd better to save list of duplicate packages and reinstall them after deleting older
yum reinstall package1_name package2_name ... packageN_name
in a case newer version haven't updated properly or damaged.
to find any problems in package database like missing dependences and duplicates.