Seeing as they already knew that someone who is Mechalel Shabbos is Chayav Misah (See Ki Sissa Sh'mos, 31:14), what was Moshe's quandary?
Rashi and Rashbam: They did not know which of the four Misos he was Chayav. 1
Targum Yonasan Sanhedrin, 105b: Moshe actually knew what to do with the Mekoshesh, 2 and he only claimed not to know in order to teach Dayanim not to be ashamed to say that they don't know. 3
As opposed to the Mekalel (in Vayikra 24:12). Refer to Vayikra, 24:12:1:1* and to 15:32:1:1. See also Torah Temimah who elaborates, and to 15:34:15:1.
See Torah Temimah, note 103.
See Targum Yonasan, who lists four cases where Moshe claimed that he did not know the Halachah - two regarding Dinei Nefashos and two, regarding Dinei Mamonos.
QUESTIONS ON RASHI
Rashi writes in Vayikra, 24:12 that Moshe did not know whether the Megadef was due to receive Misah at all, but did not know how the Mekoshesh should be killed. But R. Yehudah holds that Beis Din can only apply the death-sentence if the sinner was warned which death he will receive?
Refer to Vayikra 24:12:152:1-4.
Rashi writes that they did not know how the Mekoshesh should be killed. They should have assumed that it is Chenek, since S'tam "Mos Yumas" means Chenek?
Hadar Zekenim, Riva #1, Moshav Zekenim #1: They were unsure whether we don't learn via a Gezeirah Shavah 'Chilul-Chilul' from Avodah Zarah that she is Chayav Sekilah.
Moshav Zekenim #2: The principle S'tam "Mos Yumas" means Chenek had not yet been taught. 1
Riva: Since Hashem only told Moshe the Misah for each sin.
