Is post-hoc hypothesis an issue?
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.