On my last two runs I've noticed my lower back and butt were really sore and originally I thought it was the circuits I was doing. I still think those played some part to the soreness, but then I realized today that wasn't the only factor. The bed I've been sleeping on recently apparently hasn't been the best and I've been waking up with a sore back. Yoga really helped loosen my back yesterday so today wasn't too bad, but the soreness was still there. I felt it on my run today and it did continue to hurt more and more with each mile. I'll definitely be working on yoga before my long run this weekend so hopefully my back won't be bugging me.
Then there are generic factors that will change from day to day and route to route. Things like the temperature or weather and even the roads or trails we're running on. Some people might run better in the cold than the hot (that would be me) or you might run better in warmer weather than in cold weather. There's rain, snow, humidity and pretty much every other type of weather mother nature could throw at us that can affect our runs.
Hard roads, crumbling asphalt, muddy, or dry trails can also change our runs. I've noticed that trail running tends to my ankles sore, but then again I have weak ankles and running with all those hidden holes and what not tends to be hard for me. Plus it just seems like it takes more energy to run on trails or bad streets where you're constantly aware of pot holes or cracked asphalt.