Yeah, this is a bummer.
When you delete the preset from a layer, you're actually only deleting the "pseudo-effect" containing the sliders and other controls. Often, there are expressions on the layer that are linked to these controls. You delete the effect, the expression can't find the controls, so they throw errors.
Here are two ways to completely remove a preset from a layer in After Effects:
If you apply a preset and then undo it, you'll be right back where you started, with no expressions.
Disable the Expressions Manually
After deleting the preset effect, select the layer and press EE (press E twice in rapid succession) to reveal all properties with expressions.
On each one, click the = equals sign button to turn the expression off: ≠