Are you clicking on the cutting shape first, then the part you wish to keep?
You might try making the shape you are subtracting slightly larger than the area you are taking away - I’ve had issues with similar things when the subtracting shape has surfaces in the same plane as the main shape.
If both objects are components you can also try copying them, scaling the copies up 10x, then doing the subtraction.
Guess what guys. The senior architect I work with just informed me that we’re not going to be including this detail in the design .
But thanks for the help anyway, I’m sure I’ll need it some other time.