I had a variation on your problem: my quads were sore BEFORE I ran my 17-miler yesterday afternoon. But the reason for that was clear: I'd run two-and-a-half times up Thacker Mountain, our local mini-peak (.4 miles from bottom to top) on Friday morning and put in 8x60seconds @ 10K pace on the way home.
Even though I ran the hill repeats very moderately and took it even easier on the downhill returns, I knew I was going to be sore. I always get sore when I add solid downhills into the mix if I've been training mostly on the flats.
So my question is: did your long run have some component of significant hills in it? That alone could be the reason for your soreness.
BTW, I rarely run long runs on sore quads, preferring always to take another day off. But yesterday I thought I'd make an experiment. I was on for 18 miles--longest run of the year by three miles; I consistently run 14-15 on Sundays--and I just didn't want to postpone.
So even though my quads were sore at two miles, I continued rather than turn around. I moderated my pace a fair bit. My run took me up into rolling hills from 3 to 8.5 miles, so I got a double dose of hills. But my experience has been that I can run on sore quads if I simply treat the first half of the run like a recovery run.
I was OK by 13-14 miles and managed to pick it up a fair bit. I'm still sore today but have two short recovery days in which to get better. The experiment was successful.