Strange Distortion from Second Order Active Low Pass Filter
The LM324, while a brilliant achievement with 1970s transistors, has one well known bug - actually documented in its datasheet. This answer is based on a guess that you are running into this bug.

Some people sneer at it because of limitations like this - but it is still a fine opamp if you design to its limitations.

Its Class B output stage is specifically designed for low power but it is asymmetric : that is, it can pull up (towards V+) quite strongly, but cannot pull down very effectively. This avoids excessive current consumption where both output transistors might be momentarily turned on together (as in the bipolar 555) - a possibility given the relatively low speed of these transistors.

(See Table 6.5, page 6, Output Current section, in the datasheet - at 5V it can source 20mA but only sink 8 uA, so the pullup is 2500 times stronger)



This combination of circumstances : Class B output stage, slow transistors, asymmetric strength, gives it a particularly bad case of crossover distortion on high frequency signals, there is a region where both output transistors are off and the output voltage is effectively undefined. 

Run a sinewave at a few kHz through this filter (unit testing is as valid in hardware as it is in software!)  and you'll see large bites taken out of the output waveform.



The (documented if you look for it ... EDIT ... it's in section 7.4 on page 11, and my memory of the problem is slightly off) fix is to force the output stage into Class A, with a few kilohms of pulldown resistor to V- (I suggest 1K at this low voltage). Now the pulldown transistor never has to turn on at all (though no harm done if it does) and the much stronger pullup transistor is always in control, pulling against the resistor.

Thus the 324 is designed to be used successfully in Class B for low speed low power designs, or Class A for faster designs.

The downside to Class A is obviously increased power consumption - if that matters, nowadays you can choose a better opamp.