It's the unfortunate reality of being a male teacher - the fact that girls can very quickly call for sexual harassment if they want to get at the teacher, and it's becomes "you're guilty until you're proven innocent", especially if the girl is that close to puberty.
In this case, it's especially worse since her top was legitimately ripped off by the MC, even if MC was just trying to save her.
I do wonder if Chise used the same swimming pool Time Machine outlined in the author previous work to go back in time in this story since it been established that the two stories are connected together by a police officer character that is one of the love interests from the previous series
Chise said it herself in chapter 3:
Asaki Suzune taught her the mechanics of time travel. In case that name does not ring a bell (and I do not blame you for this, Suzune was a minor character after all),
rereading this chapter should help you jog some memories.
That said... now that everything has happened - everything Chise has been eluding to up to this point is making unfortunate sense. I still don't like how Chise was hiding this all, but even if she did warn the MC about how he would get a sexual harassment declaration - what was he supposed to do in that situation, let the poor Yui drown? Not try and even rescue her?
Not sure what Chise was hoping for by jumping back in time, but honestly, there... isn't much she could do - the fact that she is living in the same apartment as her teacher did not change just because she time-slipped. The class would eventually have found out that Chise was monopolizing MC, and Yui would act out the way she did.
I am waiting to see what Chise is going to do now - I kinda want to compare Chise and Shouta as time-jumpers. At the moment, Chise seems to be a complete foil to Shouta - Shouta may enjoy his living in the past, but his realization that he can very much change the future actually caused him to work hard to prevent that change from happening in significant ways, even though the girl he liked was willing to sacrifice her career just to be together with him. Chise... seems to just be enjoying her second run at puberty without doing much so far to change the current situation.