When your work is examined, it is usual you to need to make amendments. In this respect your thesis examination is similar to the peer review that happens when you submit work to journals. You will need to respond to all the requests for changes, both by making changes and by writing a letter that explains what you have done.
In this article, David Cook provides some really helpful advice about what to write in your response letter and how to interpret the sort of comments your reviewer might make.
A really important points he makes is that the reviewer is always right. Even if you don’t thinks so, their comments usually mean something is not clear or is missing from your document that has lead them to the wrong conclusion. Whatever it is, you must fix it. That often means thinking carefully about what the reviewer has said as it might not be obvious to you right away. It sometimes takes me a few days before I “get” their point of view.
Check out Tip 10, 11 and Table 3 in particular.
Cook, D. A. (2016). Twelve tips for getting your manuscript published. Medical Teacher, 38(1), 41-50. doi:10.3109/0142159X.2015.1074989 http://www.tandfonline.com/doi/full/10.3109/0142159X.2015.1074989