The tribes of Dan and Ephraim had some significant problems in the history of Israel. While Dan himself does not commit any great sin in Genesis (as do the sons of Leah). The blessing of Jacob in Genesis 49 was not a condemnation, although Jacob describes Dan as a “serpent by the roadside, a viper along the path, that bites the horse’s heels so that its rider tumbles backward” (Gen 49:18). In the book of Judges, however, we find that the tribe of Dan was involved in idolatry. Samson was from the tribe of Dan, during his career as judge idolatry does not appear to have ceased. The tribe of Dan migrated north to a better territory. The worshiped a “calf” after the kingdom split (1 Kings 12:25).
But would Dan be omitted because of idolatry? All the tribes were, and any of the northern tribes would have been just as involved as Dan. It is in Judah that idols were established on the temple mount and the priesthood worshiped both Yahweh and Assyrian gods. It is possible that they were the first tribe to become idolatrous, but all tribes were involved at Sinai, the real beginning of idolatry in Israel. It was, however, a Jewish tradition that Dan was the most apostate tribe (Aune 2:462, citing Str-B 3:804-805).
A common explanation for this omission is that the Antichrist would come from the tribe of Dan. As Richard Bauckham points out, for John the Antichrist is imperial Rome is not a Jew from any particular tribe (101). This is a point which must be proven yet, but the observation is enough to make us wonder if the whole tribe is removed from the list because the Antichrist would come from it!
Dan is also missing from the genealogies in 1 Chronicles 1-9. This is a more significant observation for our problem in Revelation. Perhaps the tribe of Dan failed to return from captivity and therefore lost its place in the tribes. In many prophetic passages, Ephraim becomes synonymous with the entire northern kingdom, especially in its idolatrous forms. The book of Hosea in particular uses the tribe of Ephraim to describe the apostasy of the whole of the northern kingdom.
So once again Revelation generates questions which may be impossible to answer with certainty. Perhaps the solution is as simple as the need to delete two tribes because Levi and Joseph were included.