Pay Attention to Those Twinges
The next time you feel a slight tweak in your knee while you're running, or a pull in your shoulder during your swim- PAY ATTENTION TO YOUR BODY!
Speaking from personal experience, as frustrating as it may be to be forced to take a day away from your sport, it pays off in the long run. That's not to say you need to loaf around and do nothing; on the contrary, take advantage of the same time you'd have used for your run, or ride, and do something else physical.
Get in an extra massage (hopefully regular bodywork is something that's part of the normal weekly regime anyway as it's an integral part of keeping injury at bay), an extra strength session, try a water run, or anything else physical that's not going to further tweak whatever minor injury you have, but will still allow you to get in your workout, and your workout 'high'!
Keep healthy now, so that you can return to your normal training sooner than later, and injury free!