Hi Hogans Hero,
Your muscle fibers are identical today, as they were last Thursday. So that eliminates the "Virgin Muscle" theory. Next would be the volume of your injection. The quad muscles can hold much more than 3 ML's. Now we've eliminated 2 possibilities. Since you're feeling better now and your swelling went down, we can eliminate an infection. Also if your hand wasn't steady, this would cause swelling at the spot, not from injection site all the way to the knee. So we can also eliminate the lack of steadiness.
One thing remains that could correlate with your symptoms. This is not common, however, in some cases you may have either not gone deep enough into the muscle, or simple landed in the wrong spot. Oil can leak and travel in between your muscle and epimysium sheath. With quad injections, it's likely to pool up at the knee. This can cause some irritation over expanded areas, beyond the injection site. It also prolongs/extends absorption time, leaving you with discomfort for extended periods.
If this is the case, simply avoid the very same injection site. It's merely impossible to avoid this. You just happened to be very unlucky for that moment.
Good luck buddy.