Why was Yosef so upset that Ya'akov had switched his sons?
Ramban #1: Because he was particularly fond of Menasheh his Bechor, and he was upset with Ya'akov for giving precedence to Efrayim.
Ramban #2: He was worried that his father had erred (confusing Menasheh and Efrayim), and, since he blesses them with the wrong Kavanah, his Berachah would be given without Ru'ach ha'Kodesh. 1
Da'as Zekenim, Hadar Zekenim: How does my father consider me like a fool, that I did not arrange them properly? I arranged them properly!
Consequently, as soon as his father explained that he knew exactly who was who, he calmed down. (Yakov was blessed when Yitzchak was unaware, and Yitzchak saw no need to repeat those Brachos knowingly! Perhaps there is different, for there was a Nevu'ah that Yakov get those Brachos, or Yitzchak smelled Gan Eden (refer to 27:27:1:1), and knew that the one in front of him should be blessed, whoever it is - PF.)
How could Yosef show his father a lack of respect by telling him directly that he was making a mistake?
רש"י: הרימה...ותמכה: למה הוסיף רש"י 'הרימה'?
גור אריה: קשה כיצד על ידי התמיכה ביד אביו הוא יסיר אותה מאפרים? אלא הוא הרים את יד אביו ואז תמך בה שלא תחזור לראש אפרים.