1

× We went to Kyoto, where is one of the nicest cities in Japan. 
√ We went to Kyoto, which is one of the nicest cities in Japan. 

Where is a relative pronoun acting as an adverbial of place, whereas which is a relative pronoun acting as a subject. If the relative pronoun is the subject of the verb that comes after it, then you CANNOT use where. Compare:

  • They stayed in the hotel where they had met. (Where = adverbial of place. They had met in that hotel.)
  • They stayed in a hotel which was very nice. (Which = subject. That hotel was very nice)

2

× I wanted to visit Bologna, where I had some friends there. 
√ I wanted to visit Bologna, where I had some friends.
When we use where as a relative pronoun, we CANNOT use there in the same clause. Compare:
  • I wanted to visit Bologna. I had some friends there.
  • I wanted to visit Bologna, where I had some friends.