There doesn't appear to be one consistent way of enumerating the tribes in the Bible.
Note, for example, that when Moses blesses each tribe in Deut. 33, Simeon is omitted. But the number still comes to 12 because Joseph's sons, Ephraim and Manasseh, each have their own half-tribe.
The census in 1 Cron. 4-7 doesn't seem to mention either Dan or Zebulun.
The omission of Dan in Revelation isn't the only problem with that list. It names both Joseph and Eprhaim, but not Manasseh, for example.
My personal feeling is that the issue is either textual (at some point, some scribe accidentally copied the names incorrectly) or theological (in a highly figurative book that repeatedly uses the number 12 symbolically, the number is more significant than the specific names).
Irenaeus, and a few other early fathers, suggested that Dan is not mentioned because that was the tribe the Antichrist would come from (e.g. Against Heresies 5.30.2). But it's important to remember this was only speculation on his part.