Yes, it has. There's a NTR scene with Minami early in the game and one with Yoko late in the game. I would consider the Otaku and Sheila scene NTR too, but thats me.
Well, I'd say that the Sheila and Otaku one is the only scene that
could be considered as NTR out of those three. In the first scene mentioned, if you go down that path MC doesn't really care about Minami or what happens to her with those thugs, so that isn't NTR when it doesn't fulfill the definitions of the NTR but is rather just a "rape". With Yoko it's kind of the same thing, the definitions for NTR don't get fulfilled and it's rather just "sharing" than NTR. In both cases there MC doesn't think Minami or Yoko as anything else than just a piece of meat that he "puts down" by any means necessary so they learn to follow and obey him, so they really aren't "romantic interests" for him there.
Now with Sheila it's different, as the whole story arc with her is about the mutual romance bond that they build. Does she get stolen from MC, as it's said in the classic definition of NTR? In a way, kind of. Does the MC get cucked here? In a way, he does. Is Sheila sleeping/cheating MC with Otaku? No. So it gets a bit technical here. In a way it
can be seen as NTR and therefore I understand very well if someone sees it as that, but then again it can also be seen as "only heavily flirting with NTR but still not going quite there", as that scene doesn't involve any actual sexual acts between Sheila and Otaku.
It also depends a lot on how you define NTR as you said at the end: it can be a subjective matter wether this has or doesn't have NTR, as it largely depends on how you personally feel about NTR, as for some people just another male character showing up in the same universe is considered to be pure NTR. If it is defined by the classic definition that's most commonly used in hentai, then we have the situation that I pointed out above with the examples. If it's the F95 Forum tag definition "designed to cause jealousy by having the romantic interest involved with someone other than the MC", then it once again becomes a bit technical as what is then seen/considered as "romantic interest being involved with someone other than the MC". Going with this one, I also can see how the Sheila and Otaku scene could be seen as NTR by some people. And at the same time going with this definition out of those three mentioned scenes the Sheila and Otaku one could also be the only NTR scene, as it's the only scene where the MC feels at least a bit of jealousy by having the romantic interest being involved with someone other than the MC himself.