It is common for muscles to be more sore two days after a workout, rather than the next day. The phenomenon is called DOMS: Delayed Onset Muscle Soreness. Sometimes it manifests the next day after working out; sometimes it crops up after a day's delay.
As Mark Sisson notes, we don't really know what causes DOMS physiologically:
[D]espite its ubiquity, science still hasn’t been able to nail down the precise cause of DOMS. That hasn’t stopped several popular theories from circulating.... One is that lactic acid is to blame.... Lactic acid has nothing to do with DOMS.
Another popular notion is that DOMS occurs because intense exercise breaks down your muscle fibers: you tear the muscle fibers apart with resistance training and they respond by coming back stronger than ever. The pain, then, comes with breaking down and rebuilding muscle fibers. Either that or it’s inflammation. Or it’s increased pressure on your nerves as a result of expanding muscle. There are a ton of possibilities thrown out there, and they all sound vaguely plausible, but the science is still murky. Whatever the cause, we do know that it can’t be neatly explained by a single factor. This article approaches DOMS by examining various research studies in an attempt to figure out the mystery, but the basic conclusion seems to be “DOMS simply is” (as if Descartes were a sports medicine physician).
It has been firmly established that a certain type of exercise – eccentric contraction – is more likely to cause DOMS. Eccentric contractions include walking downstairs, running downhill, and negative movements when weight training (lowering weights in a controlled motion, as opposed to letting gravity take over).