When in doubt, right click on the feature in the model tree and select Info>Feature. Here there will be a comments section that will explain the nature of the problem.
In your case the double square icon indicates that the feature is "Child of Packaged". This happens when things are referencing things that are not fully constrained. You need to go back and either "Fix" the feature, or reconstrain the original. If you dont, they may not stay where you want them.