I had a similar problem on the ESP32. (If you really want a clean signal I think that you will need an external Schmitt trigger.)

I solved it differently with a timer as follows:

static uint32_t prevT = 0;

void IRAM_ATTR IOhandleInterrupt()
{
uint32_t t = micros();
uint32_t dt = t -prevT;
if ...

This is a summary of getting a PN532 to work on the UART to help other who might have the same problem.
I used this arduino library for the PN532 https://github.com/elechouse/PN532
It basically worked first time on the SPI but I only had 3 pins left so tried to switch to UART 2.

Changed this in ...