Dear Barbara,
It's quite likely that the behaviour you describe is "By design": "question" reports (you choose the type of report from a drop-down menu close to the top right corner) will show codes applied to the children of a given node in the codes-tree.
Let's imagine you have a code called "Study Design", with three children: "RCT", "Observational" and "Other" (I'm simplifying, of course!). To capture all of the three children with a single "setting", you will use a question report and drag "Study design" into it. Let's also imagine that "RCT" and "Observational" don't have any child codes, while "Other" does have a few (to further specify what "Other" means), in this case, the interface will show the arrow you mention for "Study Design" and "Other" but not for "RCT" and "Observational", this is because the latter two don't have any child code and won't produce any result in a "Question" report.
On the other hand, "Answer" reports show codes applied to the specific codes that they include (but not their children), so all codes should show the arrow.
This is assuming no (still undiscovered) bug is gettin in the way. Please do let us know if the behaviour I'm describing is not what you are observing.
I hope this helps,
Sergio