Should I comment on a cited paper in the paper-review part of my master's thesis? I'm writing my master's thesis and began to wonder if it is acceptable to comment on some of the publications I cite in my 'State of the art' part. 

I have several papers where the results and/or methods are obfuscated. This is sadly not uncommon given the source of the author(s) are industry vendors who want to show their capabilities and domain expertise without actually revealing anything competitively substantial. The papers are all written by the engineering / research departments of various manufacturers and are published in scientific or engineering journals. 

Some of the 'errors' in their publications are surely due to out-dated methods and/or models. However some others are just plain misleading, most certainly as a way to obscure competitive information. I don't have hard facts that they are entirely erroneous due to the omission of their data, but deriving from my research I am pretty confident that some of their results don't add up.

So I don't want to just write down what they found out and how, but also comment on how correct/incorrect their results seem based on my research.

How should I best comment on these opaque industry publications?
I'm not entirely sure about what kind of publications you are talking about when you say 'published by vendors' (white papers, brochures, user manuals?). But if you are referring to scientific literature, my answer is: by all means. 

I don't se why you would refrain yourself from commenting the possible limitations or drawbacks of published methods. Just stay modest and consider the possibility that these publications came out a while ago and that the general knowledge in the field improved since then. 

Being critical, if done properly (give objective reasons), is certainly something to be encouraged at the Master's level, and yes the appropriate section for this is the "State of the art" section.