Runners accept pain as part of the sport. But not all pain is the same. You have to learn to separate the good pain, associated with the positive progression of your fitness, from the bad pain, which tends to be unfamiliar, infrequent and generally localised in one particular area of the body. It is an early-warning sign of injury, the final severity of which will be determined by how much notice you pay.
Remember to pay attention to unfamiliar pains. Ease off, and seek medical help where necessary.