Why did Moshe omit three thousand from the total (See 2:32)?
Rashi #1: He stated a round figure and did not bother to mention the small numbers.
Rashi #2 (citing R. Moshe ha'Darshan): Only the six hundred thousand who left Egypt 1 cried for meat. 2
Above, Moshe counted six hundred and three thousand, five hundred and fifty Yisraelim above twenty and eight thousand five hundred and eighty Levi'im between twenty-five and fifty (1:46, 4:48). All were born in Egypt, and other men outside these ages! Also this answer must say that Moshe ignored the excess! It seems that Moshe used the Torah's expression "Shesh Me'os Elef Ragli", just in Sh'mos (12:37) it says "k'Shesh?", and adds "Gevarim Levad mi'Taf." (PF)
See Sifsei Chachamim.
QUESTIONS ON RASHI
Rashi writes that Moshe did not bother to mention the excess above six hundred thousand. Perhaps the excess died at Tav'eirah?
Perhaps Rashi explains according to the opinion that only the Sanhedrin died there (refer to 11:1:6:2). (PF)