Non-inverting amplifier clips to unexpected voltage
This is exactly to be expected- the output voltage of an LM324 cannot swing very close to the positive rail. If you can reduce the range to something like 1V with a 3.3V supply it will work reliably for all cases over temperature etc, otherwise use a single-supply op-amp with rail-to-rail output such as LMV324 or a RRIO op-amp. 

Also note that it cannot swing below (or even quite to) the negative rail, which is 0V in your case, so you can probably depend on 0.1 to 1V with the LM324 on a single 3.3V supply, not +/-3.3.

And you definitely should not connect more than a small capacitance (as in pF not nF or uF) directly fron the op-amp output to ground- this is how you make an oscillator. Add a few hundred ohms to isolate the load capacitance.