Why my professor seems unhappy after I emailed her "thank you for the inculcation"

The word "inculcate" is associated with fostering or imparting beliefs or attitudes, particularly by repeating the same thing over and over until someone accepts it as true and unquestioningly incorporates it into their way of thinking or living.

inculcate

verb [ T ] formal uk /ˈɪŋ.kʌl.keɪt/ us /ˈɪŋ.kʌl.keɪt/

to fix beliefs or ideas in someone's mind, especially by repeating them often:

e.g. Our coach has worked hard to inculcate a team spirit in/into the players.

Source: https://dictionary.cambridge.org/dictionary/english/inculcate

This can be beneficial for the student, e.g. learning the "time tables" (5x1=5, 5x2=10, 5x3=15, ...etc) enables rapid mental calculation with little conscious effort.

Most education includes some inculcation, particularly at first when the subject is not at all understood by the student.

However it can in some cases mean imparting beliefs that are not independently provable or even beliefs that are provably incorrect.
It is therefore associated with dogma and indoctrination and propaganda in my mind (as a native English speaker) and is a relatively low (and sometimes completely unreliable) form of teaching.

This is in contrast with imparting knowledge by guidance and mentoring and inspiring, which implies that the student is being shown knowledge in a way that encourages their understanding and independent thinking and discovery.

In the case of your professor, the word would mean she is imparting the knowledge she has into you simply by your unquestioning acceptance, without requiring any understanding.

You state that she usually gives you helpful suggestions. This implies that she is suggesting a useful direction or way to discover the knowledge for yourself, and is a way of teaching you how to research and learn without anyone just telling you the answers. This is not just inculcation, even if she sometimes repeats the same thing until you understand.

I think it is more correct to use "guidance" or "mentoring" or even "inspiration" to express what you are grateful for from her.

Good luck with your studies.