Jamieson, Fausset and Brown on Ezra 1:11

11. All the vessels of gold and of silver were five thousand and four hundred--The vessels here specified amount only to the number of 2499. Hence it is probable that the larger vases only are mentioned, while the inventory of the whole, including great and small, came to the gross sum stated in the text.

them of the captivity that were brought up from Babylon unto Jerusalem--All the Jewish exiles did not embrace the privilege which the Persian king granted them. The great proportion, born in Babylon, preferred continuing in their comfortable homes to undertaking a distant, expensive, and hazardous journey to a desolate land. Nor did the returning exiles all go at once. The first band went with Zerubbabel, others afterwards with Ezra, and a large number with Nehemiah at a still later period.