That's precisely my point. The two phrases are not ironclad definitions. 'I wonder what is on their mind' is easily interpreted as 'what are they planning'. It's entirely contextual and we shouldn't be penalising people for this. Getting this marked as incorrect and having to redo it hasn't improved my Dutch at all.
I checked with a native Dutch speaker, and it doesn't have 2 meanings.
I can only mean "what do they have in mind" i.e. planning to do.
I understand your frustration, but no point in submitting alternative facts to make it fit what you think it should be just to pass the question
Better to learn the real meaning or your Dutch won't improve
Waar zijn ze met hun gedachten? That's more like "what is on their mind?"