First of all - the obvious: Don't panic.
Now, assuming your friend wants to submit asap and not rework whole sections of the thesis and take another 6 months to do that or so, I would say the following:
*Submit the thesis as is, or with an added section/paragraph highlighting some of the weaknesses of the methodology, but also explaining why it was used (e.g. the best one currently available, the one most suited for this kind of approach/problem, it is the "standard" one...)
*When it comes to the viva - know what the criticism of the methodology is, yes, where maybe errors were made, but also prepare for exactly these questions and defend the work.
Of course it is important to use the right tools, not make obvious errors, BUT it is also sometimes a question of being able to see one's own work in a critical light as well as defending the core outcomes/results/findings.
Hope that helps?!