Is it acceptable to criticise papers when writing a related work section
Think about relevance to your results

Is the particular criticism relevant to the point of your paper ?

For example "The method described in paper X works only in dry conditions, so for researching dolphin behavior it's not useful and we used a different approach described in chapter 4" is a relevant criticism and should be included.

"Paper X is a very poor and ambiguous description of the method using obsolete terminology, I had to read it five times and refer to a Klingon-English dictionary before understanding how it works" is not relevant, as most likely none of your conclusions would be based on such a sentence.    It would be relevant only if your paper is a meta-study on the readability of scientific articles, or if your paper is about historical changes in commonly used terminology in your subfield, where the faults of other papers is the topic of your research.