One of the criticisms commonly throwing that creationists is that creationism cannot be considered scientific because we can always invoke miracles to solve any problems. While this is true in principle you need to remember that creationism itself is not an alternative to evolution but an alternative to naturalism. Consequently, like naturalism, creationism is a philosophical starting point for producing scientific theories not a scientific theory itself.
Under circumstances where the Bible clearly indicates something was a direct act of God then invoking a miracle is clearly acceptable. However, invoking a miracle does not simply mean God did it and that's the end of it. A miracle would be an act of God where he is superseding or suspended natural laws to perform a particular act. Such proposals can still be considered scientific as long as they are specific enough to produce testable results. A good example of this is Doctor Russell Humphreys model of planetary magnetic fields. In this model, God starts each planet up has a ball of water and aligns the magnetic fields of the water molecules so that they form in a cumulative magnetic field. God then turned the material to rock maintaining the magnetic field which began to decay. Based on this he was able to actually predict the magnetic fields of Uranus and Neptune even though naturalistic models missed the magnetic field of Uranus.
When the Bible is not specific about a miracle or other direct act of God then we need to be extremely careful about invoking a miracle when it is not necessary. This is not to appease skeptics, but because you are likely to miss other possibilities if you jump too quickly to a miracle. The best time to include a miracle in a theory is when dealing with an event that is described in the Bible as a direct act of God, such as Creation and the Flood. Even still it is important to be specific enough that the miracle will produce testable results. Never invoke a miracle where it is simply God did it end of discussion. The door always needs to be left open to getting more specific so that testable result can be produced.
Whenever the Bible says something was a direct act of God, then miracles are going to be part of it. However, whenever possible, being specific enough to make testable predictions needs to be the goal. This is the key to being able to include miracles while remaining scientific.