Dealing with uncertainty when reviewing a paper
Yes, it is fair to raise concerns when you don't understand a paper. It is the authors' job to explain in enough detail what they did. Especially if the method used is uncommon, then it needs to be justified. That justification needs to be done in a way that it is understood by the intended audience, not just the specialist within that audience. 

Tell the authors in as much detail as possible why you think their method does not feel right. Maybe the method is problematic, and they will appreciate that feedback. Maybe they did not explain their method well enough, and they can use that feedback to pinpoint what was not clear.