Over-voltage prevention not working
It's not clear from your cartoon, you didn't post a proper schematic, but I think your wiring is this:  







simulate this circuit &ndash; Schematic created using CircuitLab

Regular diode (like 1N400x) has very slow recovery time, that means 12V will get through it for couple of microseconds which is enough to fry your MCU. Even if you use 1N4148 there is 4ns recovery time, that can be enough to fry your MCU.  

UPDATE:
There are several ways to do it properly. One of them is to use simple voltage level translator.  







simulate this circuit

Or you can use zener diode with one resistor:  







simulate this circuit

Or just simple voltage divider:  







simulate this circuit

This voltage divider is not usable in car, because voltage could be as high as 14.4V. It is usable only in circuit where you can guarantee 12V voltage level.

There are even other methods. It depends on your needs.