In Vayigash, Rabenu Bahya (also the Zohar) comments and says that the reason we had Asara Haruge Malchut because the brothers sold Yosef. However, Reuven didn't sell Yosef, so why should the corresponding Rabbi be punished for his actions?
Me'am Loez says (citing Zohar Chadash, Eichah) that R. Eliezer is counted among these ten Sages. He was arrested and nearly sentenced to death, but was miraculously spared (Avodah Zarah 16b-17a); he thus corresponds to Reuven, who played a part in the whole drama but wasn't actually involved in the sale.
Yalkut Reuveini brings several answers. Here (end of the first full paragraph) he says Reuven was actually punished for moving the beds by Bilhah.
Here he says that Yishmael Kohen Gadol (who was very handsome) was Keneged Yosef because it was Yosef's fault for inciting the brothers.
If you can't read the second one here it is written out: ילקוט ראובני על בראשית ל"ז:ח' - ואחר כך נענש יוסף על מה שגירה והסית אחיו עליו שימכרוהו על ידי אותן החלומות, לכך הוצרך שתחזור הנשמה זו בישמעאל בן אלישע כהן גדול, כדי שתסבול עונש המיתה ממש, לכן היה ר' ישמעאל יפה מאד דוגמת יוסף (חסד לאברהם עין משפט נהר כ"ה).
The Torah Sheleima mentioned in this answer, while addressing another issue (why Reuven was also fined for the sale) says that Reuven was there when they threw Yosef in the pit, which lead to the sale. He is therefore also liable.
It doesn't say it there, but not only was Reuven there, but it was his idea to throw Yosef into the pit.
the kotzker rebbe explains that at the time of throwing yosef into the pit they made a cheirem on anyone that informs yaakov, but there were only 9 brothers? the answer is hashem was the 10th. so by the asara harugei malchus one of them represented hashem. which one? the sais that we learn out something from everytime the torah adds the word "es" except for "es hashem tirau"=fear hashem" because "es" represents something close to the thing and nothing is close to g-d. rabbi akiva holds that its including the sages since they are close to g-d. since he holds the sages are close and similar to g-d he represented g-d