That would be one definition of miracles - that they are a suspension of the normal rules of physics and the universe. Otherwise they would be "coincidences" or " explainable anomolies"
Miracles are supernatural by nature, and by definition, not explainable by the normal laws of physics.
All three of the bullet points you listed are possible explanations, and all could be true for different miracles.
As for inconsistency, God is also Sovereign, and can do as He pleases if it suits His will. That's very clear in the Bible, and His miracles are always shown to have happened for a purpose. All of Jesus' miracles, if you look them up, are performed to demonstrate that He is more than just a normal man - that He is God. They all are accompanied by Him teaching or making a subtle (or not so subtle) claim to His authority.
Finally, being finite with limited (although incredible) mental capacity, we will never "understand science fully". That would mean omniscience, an attribute that is believed by Christians to be only applicable to God Himself.
It should be noted, however, that the subject of Miracles is not purely a Christian issue, nor is "supernatural" the only type of miracle possible. Miracles can, as alluded to in the first paragraph, be happy but unlikely coincidences. However, the miracles you're speaking of are clearly supernatural in nature.
Miracle From Wikipedia, the free encyclopedia
A miracle often denotes an event attributed to divine intervention.
Alternatively, it may be an event attributed to a miracle worker,
saint, or religious leader. A miracle is sometimes thought of as a
perceptible interruption of the laws of nature. Others suggest that
God may work with the laws of nature to perform what people perceive
as miracles. Theologians say that, with divine providence, God
regularly works through created nature yet is free to work without,
above, or against it as well.
In casual usage, "miracle" is seen as any event that is statistically
unlikely but beneficial, (such as surviving a natural disaster), or
simply a "wonderful" occurrence, regardless of likelihood, such as a
birth. Other miracles might be: survival of a terminal illness,
escaping a life threatening situation or 'beating the odds'. Some
coincidences may be perceived to be miracles.