If you exercise a lot you most likely have a weak spot that flares up once in a while. The most common is the knee, elbow or shoulder. It can be anywhere. And when it does flare up, you would usually work through the pain, because, well, you have done it before, and it works.
You are setting yourself up for a cycle of chronic injury that never ends well, you need to change the way you are doing things.
You may not notice it, your body compensates when there is a weakness, moving in a different way compromising your form and burning these compensations into muscle memory.
A cyclist who never stretches over time may end up walking with a slightly bowed leg stance. Over time, a shortening hamstring and calf and the discomfort of stretching the muscle coupled with longer quadriceps pulls the legs into that position, it happens over time.
Which is why that nagging pain should not be ignored.
The body produces the pain sensation in response to something that is damaging it. In the case of DOMS (Delayed Onset Muscle Soreness) that you feel after exercise, the body is telling you it needs to repair itself, and you need to give it time to do so. In the case of injury, the pain is acute, immediate, sharp and usually centralised, and it means STOP.
Rest, alternating between hot and cold compress, elevation (RICE) works well in most cases, in others, seeing a medical practitioner is necessary.
Finding out the weak links is also helpful. A lot of knee problems can be solved with stronger hip flexors for example, a lot of back problems with a stronger core. Sometimes continuous use of pain medication is not the answer, getting to the root of it will help you remain pain free long term.