You didn’t read that paper because there are lots of papers, and you can’t read them all.
You didn’t run that experiment because you ran a hundred others and it didn’t seem like that one would make a difference.
You haven’t thought about that, but you’ve thought about lots of other things.
You haven’t thought about this, but you can think about it right now and offer an opinion.
You didn’t do the thing your examiners suggest because you have reasons.
You didn’t do the other thing they’re thinking about because your supervisor told you it wasn’t worth it, and you agreed.
You didn’t do more because there is only so much time, so much effort, so much focus, so much thought you can put into a PhD. It’s big, but you can’t do everything.
When you think about why you didn’t do more, just pause and get your reasons in order. You will have them. You’ve not acted without thought. Put your reasons across. Maybe your examiners will want to talk more about it, maybe not.
Finally, you couldn’t do everything, but you can reflect on everything you did do. Remember your reasons for everything you have achieved, and don’t get bogged down in all of the things you haven’t done.