The sum total is given without any variation by Ezra, by Nehemiah (see the marginal reference), and by Esdras (1 Esdras 5:41), who adds, that in this reckoning only those of twelve years of age and upward were counted.
It is curious that the total 42,360, is so greatly in excess of the items. Ezra's items make the number 29,818; Nehemiah's 31,089, Esdras, 33,950. The original document was probably illegible in places, and the writers were forced to make omissions.

The whole congregation together was forty and two thousand three hundred and threescore. But the sums before given make no more, with Zerubbabel, and the ten principal men, than 29,829, so that there are more than 12,000 wanting; wherefore, in answer to the question, where are the 12,000? the Jews say in their chronology (a) these are they of the other tribes, who set up the altar on its bases, and gave money to the masons, &c. Ezra 3:1, this was a much larger number than were carried captive; see 2-Kings 24:14, but not to be compared with the number that came out of Egypt, Exodus 12:37. An Arabic writer (b) makes them 50,000, but wrongly.
(a) Seder Olam Rabba, c. 29. p. 86. (b) Abulpharag. Hist. Dynast. Dyn. 5. p. 82.

Let none complain of the needful expenses of their religion. Seek first the kingdom of God, his favour and his glory, then will all other things be added unto them. Their offerings were nothing, compared with the offerings of the princes in David's time; yet, being according to their ability, were as acceptable to God. The Lord will carry us through all undertakings entered on according to his will, with an aim to his glory, and dependence on his assistance. Those who, at the call of the gospel, renounce sin and return to the Lord, shall be guarded and guided through all perils of the way, and arrive safely at the mansions provided in the holy city of God.

The whole congregation together was forty and two thousand three hundred and threescore--This gross amount is twelve thousand more than the particular numbers given in the catalogue, when added together, come to. Reckoning up the smaller numbers, we shall find that they amount to 29,818 in this chapter, and to 31,089 in the parallel chapter of Nehemiah [see Nehemiah 7:66-69]. Ezra also mentions four hundred ninety-four persons omitted by Nehemiah, and Nehemiah mentions 1765 not noticed by Ezra. If, therefore, Ezra's surplus be added to the sum in Nehemiah, and Nehemiah's surplus to the number in Ezra, they will both become 31,583. Subtracting this from 42,360, there will be a deficiency of 10,777. These are omitted because they did not belong to Judah and Benjamin, or to the priests, but to the other tribes. The servants and singers, male and female, are reckoned separately (Ezra 2:65), so that putting all these items together, the number of all who went with Zerubbabel amounted to fifty thousand, with eight thousand beasts of burden [ALTING, quoted in DAVIDSON'S Hermeneutics].

The whole number of those who returned, their servants, maids, and beasts of burden. Comp. Nehemiah 7:66-69. - The sum-total of the congregation (כּאחד, as one, i.e., reckoned together; comp. Ezra 3:9; Ezra 6:20) is the same in both texts, as also in 1 Esdras, viz., 42,360; the sums of the separate statements being in all three different, and indeed amounting in each to less than the given total. The separate statements are as follow: -
AccordingtoEzra AccordingtoNehemiah Accordingto1 Esdras Men of Israel 24,144 25,406 26,390 Priests 4,289 4,289 2,388 Levites 341 360 341 Nethinim and servants of Solomon 392 392 372 Those who could not prove their Israelitish origin 652 642 652 Total 29,818 31,089 30,143
These differences are undoubtedly owing to mere clerical errors, and attempts to reconcile them in other ways cannot be justified. Many older expositors, both Jewish and Christian (Seder olam, Raschi, Ussher, J. H. Mich., and others), were of opinion that only Jews and Benjamites are enumerated in the separate statements, while the sum-total includes also those Israelites of the ten tribes who returned with them. In opposing this notion, it cannot, indeed, be alleged that no regard at all is had to members of the other tribes (Bertheau); for the several families of the men of Israel are not designated according to their tribes, but merely as those whom Nebuchadnezzar had taken away to Babylon; and among these would certainly be included, as Ussher expressly affirms, many belonging to the other tribes who had settled in the kingdom of Judah. But the very circumstances, that neither in the separate statements nor in the sum-total is any allusion made to tribal relations, and that even in the case of those families who could not prove their Israelitish origin the only question was as to whether they were of the houses and of the seed of Israel, exclude all distinction of tribes, and the sum-total is evidently intended to be the joint sum of the separate numbers. Nor can it be inferred, as J. D. Mich. conjectures, that because the parallel verse to Ezra 2:64 of our present chapter, viz., 1 Esdr. 5:41, reads thus, "and all of Israel from twelve years old and upwards, besides the servants and maids, were 42,360," the separate statements are therefore the numbers only of those of twenty years old and upwards, while the sum-total includes those also from twelve to twenty years of age. The addition "from twelve years and upwards" is devoid of critical value; because, if it had been genuine, the particular "from twenty years old and upwards" must have been added to the separate statements. Hence it is not even probable that the author of the 1st book of Esdras contemplated a reconciliation of the difference by this addition. In transcribing such a multitude of names and figures, errors could scarcely be avoided, whether through false readings of numbers or the omission of single items. The sum-total being alike in all three texts, we are obliged to assume its correctness.

The whole, &c. - The particular sums here recited, come only to twenty and nine thousand eight hundred and eighteen. Unto whom are added in this total sum twelve thousand five hundred and forty two. Which, either were of the other tribes beside Judah and Benjamin: or were such as were supposed to be Israelites, but could not prove their pedigree by their genealogies.