Unexpected behavior of the Sallen-Key second order filter
You don't have the grounding set up correctly.  Right now, you're running the circuit around the op-amp's negative supply rail so it's clipping off the bottom part of the waveform.  You need to convert this to a split rail design.  This can be done by either changing the opamp supplies from 5v and 0v to +2.5v and -2.5v or changing the ground of the rest of the circuit to +2.5v.  And try using a 1vrms input signal as 5vrms will exceed your supply rails.