Here, both Efrayim and Menasheh are attributed to Yosef. Regarding the Meraglim (13:11), only Menasheh is attributed to Yosef!
Rashi (in Sefer ha'Pardes), Moshav Zekenim, Da'as Zekenim (13:11), Hadar Zekenim (13:11): The spy from Menasheh spoke Dibah (Leshon ha'Ra, about Eretz Yisrael), so he is attributed to Yosef, who spoke Dibah, but Yehoshua, from Efrayim, did not.
R. Chaim Paltiel (13:11): Yehoshua's greatness began the fulfillment of Yakov's Brachah. He told Yosef that he put his right hand on Efrayim, for "v'Zar'o Yihyeh Melo ha'Goyim" (Bereishis 48:19). Yosef was displeased, therefore Yehoshua is not attributed to Yosef.
Meshivas Nefesh (13:11): Sometimes Efrayim is attributed to Yosef, and sometimes Menasheh, to avoid envy.
Here, both Efrayim and Menasheh are attributed to Yosef. Regarding the division of Eretz Yisrael (34:23), only Menasheh is attributed to Yosef!
Moshav Zekenim: Once only Menasheh is attributed regarding the Meraglim (refer to 1:10:151:1), also afterwards, even when the reason does not apply.
Chizkuni (13:11): The spy from Menasheh spoke Dibah, like Yosef, about Eretz Yisrael, so also regarding division of the land, only Menasheh is attributed to Yosef:
Refer to 1:10:151:3.
Pnei David (from the Ari Zal): Yosef himself was connected to Menasheh through this Nasi, but not to Yehoshua, the Nasi of Efrayim.