I can't give you a definitive answer, but I dug up some info that might help you decide how concerned you should be.
Joint heat may be a sign something is wrong. Heat is one of the cardinal signs of inflammation, so hot joints could indicate something in there is starting to act up. Inflammation could be exacerbated by high-impact cardio, especially if you're overweight (I don't know your BMI). You don't seem to have other typical signs of inflammation though (pain, redness, swelling, loss of function), so it's hard to say if you should be worried about it or not.
I found this article that compares the heat distribution over normal to inflamed joints. Check out page 495 for images of the heat distribution of normal joints and page 496 for inflamed joints. You'll see that the centers of normal joints are actually cooler than surrounding tissues. However, you should take this with a grain of salt because the measurements were taken on subjects at rest, not after exercise, and heat distribution might change a bit when you work out.
I couldn't find any research that directly compared to the temperature of muscles to that of joints during exercise, but from this thermogram from a study examining heat changes of the thigh after exercise, it looks like the area behind the knee does heat up quite a bit during exercise; however, this may not be representative of the state of entire knee joint. If you look at the images of from the study linked above, the healthy knee was much hotter behind the knee than in the actual joint.