One important thing to realize about Rashi's commentary is how often he is citing midrash. He may very well believe that these midrashim were historical. And he cites them as אגדה המיישבת דברי המקרא דבר דבור על אופניו, as he states in his commentary to Bereishit 3:8. That is, midrash which works with peshat, and answers to peshat concerns.

In this instance, Mekorei Rashi states that Rashi is getting this from Tanachuma Aleph, ot 6. Tanchuma Aleph is a variant text of Midrash Tanchuma than we have, which Rashi often. So it seems quite possible that in the text of the midrash before Rashi, the ones whom Yosef told negative reports were explicitly identified as the sons of Leah.

If so, it may be simple respect for the sanctity of the tradition of the midrash that causes Rashi to repeat the detail. That is, he repeats the midrash because it fills in the content of the dibba raa, and indeed deduces it from cues in the text. (See Yishai's answer.) But he is not about to change the midrash and strip out that detail, even if it would smooth the flow of the narrative according to the potential plot hole you identified.

And recall that not every detail of a midrash needs to be absolute peshat. It is midrash. But it is brought, in its entirety, to address a peshat concern.

As to why specifically the sons of Leah, we can think locally rather than globally. The precise content of the dibba was the subject of a three-way dispute of Tannaim, according to the midrash (as we see here). Rabbi Meir said it was ever min hachai; Rabbi Shimon said it was arayos; and Rabbi Yehuda said they denigrated the sons of the shefachot. Then, Rabbi Yehuda bar Simon combined all three. That is, he assumed all three were simultaneously true, and showed how Yosef was punished for this lashon hara.

Now, the third opinion (designated Rabbi Yehuda) has to be about the sons of Leah, who were denigrating the sons of the concubines. If so, that could be the cause of attributing all three to the sons of Leah.

One important thing to realize about Rashi's commentary is how often he is citing midrash. He may very well believe that these midrashim were historical. And he cites them as אגדה המיישבת דברי המקרא דבר דבור על אופניו, as he states in his commentary to Bereishit 3:8. That is, midrash which works with peshat, and answers to peshat concerns.

In this instance, Mekorei Rashi states that Rashi is getting this from Tanachuma Aleph, ot 6. Tanchuma Aleph is a variant text of Midrash Tanchuma than we have, which Rashi often cites. So it seems quite possible that in the text of the midrash before Rashi, the ones whom Yosef told negative reports were explicitly identified as the sons of Leah.

If so, it may be simple respect for the sanctity of the tradition of the midrash that causes Rashi to repeat the detail. That is, he repeats the midrash because it fills in the content of the dibba raa, and indeed deduces it from cues in the text. (See Yishai's answer.) But he is not about to change the midrash and strip out that detail, even if it would smooth the flow of the narrative according to the potential plot hole you identified.

And recall that not every detail of a midrash needs to be absolute peshat. It is midrash. But it is brought, in its entirety, to address a peshat concern.

As to why specifically the sons of Leah, we can think locally rather than globally. The precise content of the dibba was the subject of a three-way dispute of Tannaim, according to the midrash (as we see here). Rabbi Meir said it was ever min hachai; Rabbi Shimon said it was arayos; and Rabbi Yehuda said they denigrated the sons of the shefachot. Then, Rabbi Yehuda bar Simon combined all three. That is, he assumed all three were simultaneously true, and showed how Yosef was punished for this lashon hara.

Now, the third opinion (designated Rabbi Yehuda) has to be about the sons of Leah, who were denigrating the sons of the concubines. If so, that could be the cause of attributing all three to the sons of Leah.