I believe the passages here relate to Rabbi Yonatan the Amora, as opposed to passages about Rabbi Yonatan the Tanna.
Gd agreed with his explanation of the story of the Concubine at Givah, as well as that of Rabbi Evyatar: Gittin 6b
Exchanging Rabbi Yochanan for Rabbi Yonatan in debates in the tractates of the Holidays: Succah 4b; Megillah 7a
Rabbi Chiyya and Rabbi Yonatan walking in a cemetery, and their dialogue on the awareness of the dead: Berachot 18a-b
A man gave away his property to his children, and Rabbi Yonatan forced the children to support their father, even though that was not the law. The father came and kissed Rabbi Yonatan's foot: Ketuvot 49b-50a