Why was Moshe angry?
Rashi (in the original text citing the Tanchuma): It does mean angry; it means that he was deeply upset
Even though he did answer their other accusation
Which Minchah was Moshe referring to?
Rashi #1 and Targum Yonasan: He was referring to the Ketores that they would bring the following day. 1
Rashi #2: He was referring to the individual portion that each person has in the Korban Tamid. 2
Ramban (citing Targum Onkelos): Seeing as they wanted the Kehunah and to sacrifice the Korbanos, Moshe Davened that Hashem should decline to accept any Korban that they might bring on the Mizbe'ach 3 and any Tefilah that they might offer.
See Ramban's objection to this explanation.
Rashi: He prayed that the fire on the Mizbe'ach should not burn it. See Ramban's objection to this explanation.
What was he referring to when he said "Lo Chamor Echad meihem Nasasi."?
Rashi (citing Targum Onkelos) and Targum Yonasan 1 : He was referring to a transport tax
And what did he mean when he concluded "ve'Lo Hare'osi es Achad meihem".