Why does it say "Shama Hashem"?
Radak: Even though they said so in their hearts, Hashem heard.
Why does it say "v'Esh Niskah v'Yakov"?
Rashi: This is like "u'Vi'aru v'Hisiku" (Yechezkel 39:9); it is an expression of burning - "va'Tiv'ar Bam Esh Hashem" (Bamidbar 11:1).
Radak: The fire of His anger burned against Yakov. Malbim - Yakov is the lower part of the nation. "Va'Tochal bi'Ktzei ha'Machaneh" - the lower ones.
Why does it say "Af Alah v'Yisrael"?
Radak #1: The matter is repeated in different words.
Radak #2: The verse discusses two matters - the [complaining] at Tav'erah, and [lusting for meat] at Kivros ha'Ta'avah. They are the same place, just the Torah gave it two names based on the two episodes. "V'Esh Niskah v'Yakov" refers to the former, and "Af Alah v'Yisrael" refers to the latter - "v'Af Hashem Charah va'Am" (Bamidbar 11:33). Both sins were based on lack of Emunah; they were punished for both. The complainers said "Nishlechah Anashim Lefaneinu v'Yachperu Lanu Es ha'Aretz" (Devarim 1:22). They did not believe that Hashem would fight for them without [them making] war. Also requesting meat was due to lack of Emunah - "ha'Gam Lechem Yuchal Tes" (verse 20).
Malbim: This is anger against the choice Yisraelim. Also they quarreled about meat - "va'Yashuvu va'Yivku Gam Bnei Yisrael va'Yomeru Mi Ya'achilenu Basar" (Bamidbar 11:4). The anger was not due to lust for meat; refer to 78:22:1:2.