Are these Bible verses referencing UFOs? Ezekiel 1:16:


  This was the appearance and structure of the wheels: They sparkled like topaz, and all four looked alike. Each appeared to be made like a wheel intersecting a wheel. 


Exodus 13:22:


  Neither the pillar of cloud by day nor the pillar of fire by night left its place in front of the people. 


2 Kings 2:1:


  When the LORD was about to take Elijah up to heaven in a whirlwind, Elijah and Elisha were on their way from Gilgal.


Do these, or any other verses in the Bible, refer to UFOs, in the sense of extra-terrestrial, or extra-dimensional vehicles?
Depends on how UFO is being defined. Extra-terrestrial? God and his angels are also extra-terrestrial! But, I assume you are meaning life outside of Earth, but not including heavenly beings. In which case, then, these cases you mentioned aren't "UFO's"

In the first example, the things being referred to can be seen in verse one:


  Now it came to pass in the thirtieth year, in the fourth [month], in the fifth [day] of the month, as I [was] among the captives by the river of Chebar, [that] the heavens were opened, and I saw visions of God.


This where the wheels came from. It can be clearly seen that, the wheels, came from Heaven. Being so, it would have been a heavenly object, thus, disqualifying it from being a UFO. 

The second example given, was actually the angel of the Lord, not any extra-terrestrial object, thus, not a UFO either.

A whirlwind is obviously not an extra-dimensional vehicle, as whirlwinds appear everyday. 

What might pass of as an extra-dimensional vehicle, could be the "chariots of fire, and the horses of fire" that took Elijah up into heaven:


  1 And it came to pass, as they still went on, and talked, that, behold, [there appeared] a chariot of fire, and horses of fire, and parted them both asunder; and Elijah went up by a whirlwind into heaven.


However, it could be argued that, as these are coming from Heaven, these are still heavenly beings or objects, and thus, not UFOs