I suggest that your first presumption about the student and his/her work is that it is well done. After all, it was taken under the direction of the advisor. However, depending on your field, it may not be possible for you to understand everything in the thesis. That is natural in Mathematics, for example, as people with different specialties use somewhat different thought processes. But, for a Master's level thesis you should understand most of it, at least in general.
Read the thesis and do a mark-up as you go. Work from a paper copy if possible. Be sure to mark things that you don't understand unless that amounts to nearly everything. Marking grammar etc is also helpful. Write your name on this document and at the end of the presentation session give it to the candidate. They will find it very helpful.
During the presentation, see if the questions you marked in the thesis are answered or not. It is easy to check them off as you go.
As to the questions you ask, since you are new at this, stick to asking for clarification on things you didn't understand in the work or in the presentation. Ask for simple, not complex, explanations. Some candidates won't be very good at this and will be overly pedantic since they, too, are new to this.
An experienced person (senior professor) might want to ask a more complex question of the candidate to explore either deeper knowledge of the topic or even general knowledge of the field, but I'd stay away from that sort of thing as a newcomer to this process.
You probably work on different problems than the candidate did so you have a somewhat different perspective. One thing you might suggest is future directions for the candidate. I would prefer to to this by annotating the markup rather than bringing it up in the presentation, however. You can be helpful.
Assume it is fine. Ask for clarifications. Be as helpful as you can. As a beginner, keep negative comments "offline" unless something is essentially wrong. But if you think something is seriously wrong, you can, perhaps, communicate that before the presentation. Perhaps to the candidate's professor through your own, rather than directly.