Why did Moshe omit 3,000 (See 2:32)?
Rashi #1: He stated a round figure and did not bother to mention the small numbers.
Above, Moshe counted 603,550 Yisraelim above 20 and 8,580 Leviyim between 25 and 50 (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 Shemos (12:37) it says "k'Shesh
Rashi writes that Moshe did not bother to mention the excess above 600,000. 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)