Same issue in my clan. I have no clue what to do. I have people playing 3 hour matches and not being counted. How long does it take Elite to iron out all of these bugs?

The member has to be a part of your clan before you enlisted you clan in the operation. If he joined after you enlisted, He will not count. Here is the quote from the Clan Operations FAQhttp://support.activision.com/articles/en_US/FAQ/Clan-Operations--FAQ/?q=clan+op eration&l=en_US&c=Platform%3AElite&fs=Search&pn=1

Will my score be counted if I join a Clan during a Clan Operation?

Your Clan stats count toward the last team you were on during enlistment.

• Joining another Clan during a Clan Operation

If you were enlisted in Clan A but joined Clan B in the middle of a Clan Operation, only your score with Clan A will count.

• Leaving a Clan during a Clan Operation but not joining a new Clan

If you were in enlisted in Clan A during a Clan Operation but left Clan A before the end of an Operation and didn't join a new Clan, your score will count towards Clan A.