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Efrayim and Manashe both have different trope from the other ten, by the way.  With Manashe there are extra words that the trope has to account for, but it's interesting that Efrayim, without that constraint, nonetheless has different trope too.

I asked and answered a duplicate to this question before remembering this one, so I'll move that answer here.  Like the Ramban cited in [this answer](https://judaism.codidact.com/posts/282070/282178#answer-282178), Chizkuni also ties it to tale-bearing -- something Yosef and Manashe have in common.  [Chizkuni on Bamidbar 13:11](https://www.sefaria.org/Numbers.13.11?ven=The_Contemporary_Torah,_Jewish_Publication_Society,_2006&vhe=Miqra_according_to_the_Masorah&lang=bi&with=Chizkuni&lang2=en):

> Even though on numerous occasions the tribe of Joseph is equated with the tribe of Ephrayim (seeing that Yaakov had told Joseph that he outranked Menashe the older), here Joseph and Menashe are paired, seeing that both had become guilty of slander. Joseph had slandered his brothers to his father, and the prince of Menashe had slandered the land of Israel. There are several instances where Joseph and Menashe are equated precisely because the context of the story supports that interpretation. (Compare Numbers 34,23, Joshua 17,1) In Joshua 17, the subject is the distribution of the land to the various tribes, and it was these lands that the prince of Menashe had slandered in joining the majority report of the spies.

Chizkuni doesn't say, but the fact that the representative of Efrayim, Hoshea bin Nun, was one of the two who did *not* speak against the land seems relevant.  Not only did Yosef and Manashe engage in slander, but the representative of Efrayim explicitly did not.  Both are from Yosef, but the text only adds Yosef to one of them.  Chizkuni's reasoning seems consistent with that.