I have played quite a bit of the game with the ultimate edition patch and I noticed that during some lines the voice over quality changes drastically.
It also doesn't seem to be character specific as this has happened during Rin's and Illya's lines.

Two examples:
In unlimited blade works, in the 12th Day during the "Strategy meeting", if you choose to Rin if the church has a secret passage, Rin proposes the idea of teaming up with other masters. Rin's lines "It's not good enough to be called an idea. Look, it's obvious that we can't beat Caster by ourselves, right? So we have to increase our forces." sound very different in quality than the line just after them.

During the 16th Tiger Dojo, Illya's lines "And a special tip for those that came here without seeing any ending!" "Um, you can't clear Rin no matter what you do during your first play." "It'll be smart to fight along with Saber as her Master at least once." again sound much different from the lines just before them in terms of quality.

I cannot think of any reason as to why these lines sound different. Is this related to the original Realta Nua or the ultimate edition patch? Is it a software bug in the game or are these specific recordings just awful? Are these even recordings or crappy deep fakes of the voices?