In the Mishna at the beginning of the perek (89a) Rabbi Shimon ruled that roofs, gardens, yards, etc. are all considered a single private domain, and therefore people can carry between them on Shabbat, regardless of who the owners are. On our daf we find that both Rav and Shmuel rule like Rabbi Shimon, although they disagree as to whether the rule applies in all cases. According to Rav, Rabbi Shimon’s ruling is applied only if the individual owners did not make an eiruv for each courtyard. If, however, an eiruv was made for each courtyard (but not between all of the courtyards), we fear that someone will carry from his house into the courtyard, and from there into other yards or gardens, which would be forbidden. Shmuel disagrees and rules that even when individual eiruvin have been made, we can make use of Rabbi Shimon’s ruling and permit people to carry between roofs, etc.
This odd expression is so strange that Rashi simply says that it should not be included in the Gemara. The Tosafot do, in fact, believe that it should be included in the Gemara, pointing out that similar expressions are found in Midrashei halakha like the Torat Kohanim. A number of explanations are offered as to what it might mean:
Rabbenu Shmuel understands that Rabbi Yohanan is responding to Rav and is saying, “who whispered to you that there is a difference between cases when an eiruv has been made and when it has not?”
Rabbeinu Tam explains that Rabbi Yohanan is responding to Shmuel, whose rulings in other areas seem to indicate that he would take a stringent position when interpreting Rabbi Shimon. (Incidentally, in the Jerusalem Talmud Shmuel is quoted as ruling that when eiruvin have been made we do apply Rabbi Shimon’s ruling permitting people to carry from one roof to another). Thus he is saying, “who whispered to you that in this case there is no reason to differentiate between cases when an eiruv has been made and when it has not!” indicating that he is impressed that Shmuel knew to rule leniently in this case.