A Moodle was installed originally on 2.2.1. Later was upgraded to 2.2.2 and recently to 2.2.4+.
All course content was built on initial version, and was replicated to more course using backup and restore and later modified on then new different instances.
The result was duplicate records on the following tables: course_completions and course_completion_crit_compl.
The upgrade to 2.2.4 removed duplicates from course_completions (nearly 2000 duplicates), but not from course_completion_crit_compl (it has 2500+ duplicates).

This causes various issues with course completions and reports.

See this related issue:
http://tracker.moodle.org/browse/MDL-27114