Is post-hoc hypothesis an issue? I was asked to serve as a reviewer in a peer-review process.  I remarked some issues and suggested a minor revision to the editor.  Now I received the revision back and generally think the authors did a good job revising the manuscript. The field is psychology. 

There is one issue that I was not sure about. That is, the authors changed their hypotheses between drafts. This has something to do with the way they treated their data. In the first draft, the experiment provided data from two instruments (very similar instruments) and were analysed separately. Hypotheses were formulated separately for the two instruments. 

Now, in the 2nd draft the instruments were combined and the data treated as coming from one instrument. Hypotheses were adapted to these new circumstances, but also were partly contradictory to previous hypotheses because then, the authors expected some differential results from the two instruments.  

I am not sure how to judge this. Is this a big issue or just a minor thing?  Why is it an issue at all?  I have a feeling that this not too uncommon in my field (psychology), I mean to treat hypothesis testing somewhat lax.  I believe that in grad school I learned that hypotheses have to be stated before conducting the experiment and cannot change. But I was googling a little about this topic and did not find anything that would indicate that post-hoc hypotheses are a bad thing.
There is substantial divergence between fields and individuals to what extend twiddling with the original hypotheses post-hoc should be tolerated. Defensible positions range from "it's not a big deal if the experiment / write-up still makes sense with the new hypothesis" to "hypotheses shall never be changed". Only you can tell what your and your field's methodological stance on this is.

As Boris says, the main issue to avoid is "p-value hacking". That is, it should not be that the authors decide that whatever they find support in their data is redefined to have been their hypothesis all along - while exploratory research per se is not bad, it is distinctly different from hypothesis-driven research and should methodologically not be sold as such. You will need to evaluate whether this has happened for your manuscript. If the answer is "yes", this is certainly grounds for rejection.

However, from your explanation, it sounds to me like the authors did more of a technical refinement of their hypothesis, without changing the nature of it. If that is true, it sounds somewhat nit-picky to reject a paper on this grounds. I tend to be of the opinion that methodology should be considered a means to an end, not a strict rulebook that needs to be followed to the letter even if there appears to be no reason for some of its details in a specific case.