We've come to be very familiar with the operation of an MRI and they are useful in a lot of different ways to examine and detect injury or damage to the body, and the brain is no exception. But remember that many times damage to the brain occurs on a very very tiny level of the brain that is very difficult to detect.
MRI's come in various strengths. A person may have a well documented brain injury from a physician but the MRI may not be strong enough to actually detect the physical damage done to those neurons within the brain.
So, sometimes using a stronger magnet can produce a clearer picture but many times well documented clinical evidence of brain injury is simply not large enough or big enough to be detected in an MRI. So they are not infallible.