How did they rebel in the Midbar?
Malbim: This includes all their sins in the Midbar until the Meraglim. They transgressed Chukim and Mishpatim - all the Mitzvos.
How did they not go in His Chukim?
Rashi: They tested me with the Egel and in Refidim [they slackened] from receiving 1 the Torah, and they left over from the manna.
Radak: He commanded them at Marah "Sham Sam Lo Chok u'Mishpat 2 " (Shemos 15:25). They transgressed them - "Ad Anah Me'antem Lishmor Mitzvosai v'Sorosai" (ibid. 16:28).
The Midrashim (e.g. Tanchuma Beshalach 25) say that they slackened from Torah, i.e. engaging in Mitzvos that they already received. Rashi implies that Hashem wanted to give to them more (or perhaps the entire) Torah, and they did not want. (PF) They repented before coming to Har Sinai (Rashi Shemos 19:2).
Sanhedrin 56b: I.e. Shabbos, monetary laws and Kivud Av v'Em.
How were they Mechalel Shabbos [Me'od]?
Rashi: Some of the nation went out to collect manna on Shabbos 1 . Radak - this was the first Shabbos!
They did not find (Shemos 16:20)! Perhaps they transgressed Hotza'ah of Kelim in which they planned to collect it. Why didn't Rashi say that the Mekoshesh transgressed? Perhaps his execution totally atoned for his sin, and it would not be mentioned. Alternatively, "Chilelu" implies more than one person. Tanchuma (Shemos 10) says that Dasan and Aviram went out. (PF)
