This issue could be related to targeting (find out more here). When Squared syncs with an account it breaks all the targeting down into what we call "Targeting Groups", these are the unique sets of targeting in your account. You can see the targeting for the account under Manage --> Targeting.
We use targeting groups to allow the adding of queries to different sets of targeting. For example if you have split your campaigns by device, you would want the same keyword in your mobile, desktop and tablet campaigns and they are not considered duplicates. So, if a high spending query was being triggered in your desktop campaign, even if it was live as an exact match keyword in your mobile campaign, we would suggest adding it as an exact match in your desktop campaign.