Sallen-Key filter using LM358 doesn't act as supposed to when fed a 31.25 kHz PWM
This looks like crossover distortion in the amplifier- it's really not fast enough to respond to the 30kHz input. You can try a pullup resistor of a few K on the output, but that will prevent the output from going all the way to ground, unless you have a negative supply. 

This kind of thing (dependence on op-amp output impedance) is one of the reasons why I don't particularly care for S-K filters. You might do better with a passive filter, at least for the first stage where you've got very fast edges.