Opinions vary as to how necessary it is to include sections on "Potential Pitfalls" (I also see the more neutral "Alternative Considerations") in the Research Plan narrative of an NIH grant proposal. Of course, opinions also vary on how much you should devote to a discussion of "Interpretation of Anticipated Results". Nevertheless, many study sections (including all the ones I've sat on) expect to see this and will ding you if you don't include it. It is way up there on the list of StockCritiques, in my experience.
When discussing "potential pitfalls", is it reasonable to say "X isn't a problem b/c..."? To show I've thought thru problems for ea aspect?
My suggestion is that you do not want to come across* as "This is some possible outcome that would really screw with my hypotheses and interpretations. However it ain't gonna happen, because of blahdeblah blah, so let's not worry about that."
No way. If this IS the only answer, find some other "potential pitfall" to talk about**. Seriously.
What you want to do is to accept that a pitfall that you identify (or is overwhelmingly obvious) could possibly occur. Fully accept. And give a description of how this would change your interpretation of the results of the Experiment. And how it would change the subsequent line of attack. Perhaps even show how the working hypotheses might need to be modified.
By no means should you simply dismiss any possible adverse or unexpected outcome as impossible or so unlikely as to not be worth your time considering. That way lies triage.
*And I am not entirely positive this is what biochemme meant, but it is worth addressing even if she didn't. Yeah, I've seen this type of stiff arm in too many proposals....
**You get to choose which pitfalls you talk about. Choose wisely. You can't leave something that is overwhelmingly obvious to any reader ignored..but then if you have too many of those your plan needs some serious re-design anyway. As always, the audience here is not your entrenched detractor who can find and obsess over the least likely adverse outcome if she so chooses. Your audience is your advocate. You are trying to give this reviewer enough ammo to say "The applicant appropriately considered potential adverse outcomes and pitfalls and has a reasonable plan to advance should they occur" or similar.