When saying 'She can't understand this problem', does that mean;

'She tries to understand the problem but still cannot manage to'
'She doesn't have enough mental capacity to understhand the problem'
or both?

Who knows why she can't understand it? Maybe the person expressing it said it very poorly. Maybe it uses vocabulary she hasn't learned yet.

The only thin you know for sure is that she doesn't understand -- not the barrier that keeps her from understanding.

Indeed, it's difficult to define it. It depends everytime on the context. But I would tend to the first sentence. She has enough mental capacity and she has another opinion to the problem.
 BarbaraPA's reply was promoted to an answer.