Any part of a transaction which cannot be done online is a huge red flag for not getting full 100% EQM's. I'm sorry that you had to find this out the hard way. I agree with the other posters above that you don't really have any recourse with respect to earning 100% EQM's.

My only suggestion if the additional EQM's are that important to you would be to call CO and find out how much it would cost to upgrade the itinerary to a fare that would enable you to earn full EQM's -- or at least enough EQM's to hit that next level of status, if that is your goal.

You also mentioned SkyTeam partners, but you did not specify the dates which you are flying. Are you flying prior to October 24? You will not be able to earn any CO EQM's on SkyTeam partners after October 24.