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It is the author's job to be comprehensible, clear, and correct. If the paper falls short in that regard, you are doing the author and the editor a favor by asking for clarifications.

If you are feeling at all unsure, you could always say things like "I'm afraid I got a bit confused by Y", "I was not able to see how the proof of Lemma 1 handled infinite sets, would you please elaborate", "Would you please say where in [X] result Z can be found?", etc.
http://mathoverflow.net/revisions/82348/list
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