Higher than expected voltage in RC low pass filter
You'll need to know the impedance of your ECU's voltage measurements.
Your circuit only works if your VM1 is really electrically &quot;not there&quot; (i.e. an open end) or has a very high impedance compared to your 1 MΩ (say, 100 MΩ).
It's likely that's not the case. Assuming it's just a slow ADC input on a specialized microcontroller, I'd expect some 100 kΩ impedance, maybe. Maybe less.
In that case, you'd have to scale down your whole RC filter: the resistor shouldn't be larger than 1 kΩ, and because you reduced the resistance by a factor of 100, you need to increase the capacitance by a factor of 100 to 100 µF to get the same frequency behaviour.
Seeing that you get a higher voltage then you expect: There's something resonant going on here. So, maybe your signal description is plain wrong (which might be the case - a sensor that needs to be read accurately across a whole car chassis would usually not be a voltage source, but something digital, or a current sink, or a typical 4-20 mA industrial sensor thing).
Also, never discount the possibility that you're not measuring what you should be measuring – diagnosing that, however, would probably take an oscilloscope with a high input impedance.