In essence, the PP system calculates the rating by a background simulation of driving the car.
If the car is literally impossible for the AI to drive, you get ⚠️. That means that while things like suspension and gearing settings don't directly affect the PP calculation (power, weight, tyres, downforce do), they can cause the ⚠️ to appear. It sounds like you're having issues driving it yourself, so potentially there's an issue with how you have the suspension set up or you're using tyres that are too grippy for the suspension.