The waveforms show mainly one thing: Either the "LPF" itself is useless, the signal is completely bypassing it, or the measurement is not showing the signal correctly, e.g. due to unsuitable probing.
The filter values suggest, that the signal is very slow, so completely supressing the interferences with a filter should be easy. So if the waveform does show the real interfering signal or not, it's apparently bypassing the filter. If so, it's mainly a matter of circuit layout and ground wiring.