UFO's are the king of controversy because their physical characteristics appear to violate our known laws of physics. Most often they are attributed to balloons, kites, methane gas eruptions, experimental aircraft or other explainable events. Some of the more exotic sightings can sometimes be explained by government black projects or secret military technology.
The truth is, there are physical laws that are still mysterious to scientists and physicists. We suspect there could be additional dimensions and new laws to be discovered, so we may not know what we may not know outside the high-security black projects which the military must keep concealed.
Scientists have found that with quantum mechanics, particles can suddenly appear out of nowhere, in space and just as quickly as they appeared, they disappear. We most likely will be able to detect and explain the nature of dark matter and energy one day and buried within this new information we may find answers to some of the mysterious sightings that have been reported. Of course, we must also consider that some of the sightings and unexplained experiences are of the spiritual realm.
There are basically five classes of UFO encounters:
1. Witnesses to events that are later determined to be under the influence or control of legal or illegal pharmaceuticals, alcohol or mental illness and generally those are easily discounted.
2. There are sightings that can be explained by everyday occurrences such as balloons, electrical anomalies, and other such objects or events. Today, we have to contend with inexpensive hobby drones, pranks etc. While sometimes difficult to prove, usually some of the sightings can be assumed to be due to these causes. To this should be added the intentional pranking or misleading of the public with photographic trickery through manipulation of digital imagery. Some of this is quite compelling.
3. Experiences which are more difficult to prove and could be part of "Black Projects" or top secret aircraft programs. There are rumors that aircraft may possess advanced developments in anti-gravity or other new technologies that could be incorporated from developments in quantum mechanics. We must keep in mind aircraft like the SR-71 spy plane and other stealth craft were in use for nearly 20 years before being revealed to the public.
4. Of course, there is the difficult to explain, visual, first-hand reports from astronauts, airline pilots, military personnel, police and other extremely credible individuals as well as mass encounterers by many individuals. Along with this group is sometimes verifiable evidence that can not be explained by known physical or natural causes. This can sometimes include physical evidence to plant life, structures or interference with electronic equipment as well as unexplainable radar signatures which elude any known craft or speeds.
5. This last group constitutes a much smaller portion of sightings, however, these accounts do not have a plausible explanation. Some argue that these occurrences can only point to an advanced civilization or even time travelers from our future. Some even claim that these sightings and experiences are visitations of "Ancient Astronauts" or "Ancient Aliens", which they claim are members of advanced civilizations that have come to intervene, help, confuse, exploit the people of Earth. The evidence of this is much less compelling and the misinterpretation of history and evidence is often extreme.
Let us look at the later class of possibilities. If an advanced civilization has bridged the speed of light barrier and has been visiting us for years, why would they not have contacted us? After all, that is a long road trip to just come and turn around and head home without at least saying hello. Do not forget the closest possibility star is 4 light years away and a civilization would have to defy all odds both with living conditions and intelligence.
Obviously, with as many or more than an estimated 1,000,000,000,000,000,000,000 stars in our observable universe, the possibility exists, that it could be another stellar civilization. Even if one day, a ship of aliens lands in Washington, DC and ask to have lunch with the President and other world leaders, this should not affect the Christian's faith in God at all. There is nothing that would prevent the existence of other civilizations that God has created.
It must be pointed out that even though there are many potential star systems out there, the likely hood of conditions being close enough for even close forms of life is extremely low. Even if intelligent life were able to evolve, unless that intelligent life had limbs and some form of digits or fingers, building a civilization and in particular intricate spacecraft would be impossible.
Consider the US launched the first Voyager mission in 1977 and has been traveling around 38,000 miles per hour and only reached the edge of our solar system in August 2012. It is on it's way to the next scheduled body, a star that is 17.6 light years away, it will arrive there in about 40,000 years. If it were to reach the star in 17.6 years time, Voyager would have to improve its pace by a factor of 17,647 times and overcome the barriers of near light speed at 670,615,200 mph. Of course approaching the speed of light presents a problem for fuel. As you approach light speed, the fuel requirements inflate exponentially and approach infinity.
Another problem with traveling at close to light speed would be slamming into some space object and it could be as small as a grain of sand. It would be like jumping in a Ferrari and racing through New York city doing 200 mph, you would be on the other side of an object before you knew you had crashed into it.
It is a bit telling that sightings have occurred in pre-space age and aircraft ages. It could also be argued that these potential visitors are attempting to be elusive and in some cases would appear to be attempting to badger or taunt observers for a reaction. Encounters like this have been reported with airforce and military members and law enforcement throughout the world.
While it would not be inconsistent with Biblical theology that other life forms are out there, it is also very plausible that what people are witnessing could be of the spirit world. When angels are referenced in the Bible, many times they appear in human form and thus if they have that capability, it could be argued that a craft of ship could exist as well.
Some would argue that these sightings are efforts of the demonic realm to confuse, mislead, fool or mystify individuals on earth into believing that they are visitors from another civilization. Since the Bible does teach about spirits, demon's and angels, this could very well be something of a spiritual, extra-dimensional realm which would fit some of the exotic sightings and experiences.
The Bible clearly teaches of a Heavenly host, angels, and demons. In fact, we are clearly taught that even angels are among us without our knowledge. We have possible examples in the many NDE's & OBE's that have been reported. The Bible does not rule out angels or demons using some sort of craft to visit or expose themselves to our senses, so it is entirely possible that the wonders (or craft) that we see are angels or demons exposing themselves via our 3-dimensional world, potentially from additional dimensions.
The Bible has this to say:
 Let love of the brethren continue.  Do not neglect to show hospitality to strangers, for by this some have entertained angels without knowing it. Hebrews 13:1-2
The heavens are telling of the glory of God; And their expanse is declaring the work of His hands. - Psalms 19:1
For by Him all things were created, both in the heavens and on earth, visible and invisible, whether thrones or dominions or rulers or authorities-all things have been created through Him and for Him. - Colossians 1:16