It is quite believable that missiles of those two systems are completely different in terms of acceleration and maneuverability. Just look at their sizes :-)
This article explains that S-400/500 are intended as eventual replacement of existing ABM systems around Moscow. We need to remember that even A-135 was designed for nuclear warheads, so it never needed to hit the target; "close enough" was just as good. But nuclear warheads were removed from those missiles many years ago, and the resulting configuration is probably marginal. By the time S-500 are deployed those A-135's will be at least 20 years old, a good age for retirement.
Or could the S-400 still has technical problems. So the Russians are adding more Pantsir-S1 to make up what the S-400 lacks.