GPIO over voltage input protection
The MM3Z3V0T1G is designed to "regulate" to about 3.3v when 5mA is driven through it.  

3.3v * 0.005A = 16.5mW typical quiescent dissipation. The package can dissipate a maximum of 300mW of power. 300mW/3.5v = ~86mA maximum sustained current.

To get 5mA to flow through it, R45 will need to be dropped from 10kΩ to ~0Ω because the supply voltage is the same as the regulation voltage... but then it will be impossible to drive the input pin low.

Try R45 = 220Ω and R10 = 0Ω.  This should give >3v to the input when the switch is not active, and 3.3v/220Ω = 15mA through the switch when closed.

Reducing R45 and R10 will drastically negate the effects of C36 to "debounce" the switch. Either increase C36 or create a separate R-C filter after the zener.