Issues with a Sallen-Key low pass filter for turning a PWM into a DC voltage
The awful truth is S&amp;K LPF has problems with suppressing the HF spectrum of the square edge is f-3dB=0.35/tR  is far greater than the 1MHz or so GBW of the Op Amp.  So a spike passes thru and then gets integrated and then held by the low impedance DC output.
Negative feedback is unable to deal effectively with a fast square wave input.
Solution?
Don't use feed forward/back for a LPF using  fast rising square wave input that exceeds the bandwidth of the Op amp where gain &gt; ~10 to 1000 depending on noise tolerance.
Use a 2 stage passive LPF.
56k : 220 nF then 560k : 22 nF  to a Unity gain buffer with matching feedback R if you care about IiR= input bias offset
When you design something , define all your requirements (SPECS!) or acceptance criteria.
You gave an unspecified LPF somewhere around 1 to 10 Hz with a rise time of 0.35/f-3dB for 10 to 90% tR.  That's pretty slow.
If you need a &lt;1 ms rise time, then consider an dual slope integrator with S&amp;H and reset or dual S&amp;H. The dual slope makes it independent of frequency and if biased to Vdd/2 with a CMOS OA, you can get full scale 0 to 100% PWM for 0 to Vdd.
e.g. Noise, DC Offset, tolerances, Rise time