Hi Steve,
In practise critiques of papers in the way you describe are rarely published in any scientific journals. Where the findings of a paper are questioned it is usual to do so through the publication of another paper, offering further evidence which may lead to alternative conclusions. The scientific community is then left to judge the validity of the two bodies of work and carry out further investigations to clarify the situation.
If however you are not ready at this stage to offer alternative evidence by way of a formal paper and just want to test out your thoughts on specifically why “the process used in the paper to generate the estimates from the measured data” might not be sufficiently robust, even though the referees of the paper apparently thought they were, then I have found an informal discussion with ones peers as could be done here, can be a very effective in clarifying ones thinking.
Cheers
Robin