I haven't done mine yet, so others will probably offer better advice. But based on what you've said I would suggest two things. First, (and this is probably really hard or impossible), try not to worry, as that won't gain you anything (and I know when I am in your position in under a year's time I will think that is ridiculous advice as well). Second, I would write a list of the key issues that there were with my research (such as the one you have described) and bullet point what you will say as a robust defense (where appropriate) or very clear explanation as to why it was the case, what impact you think it had, how it could have been done differently etc.