Manufacturer's page of the VL53L0X : https://www.st.com/en/imaging-and-photonics-solutions/vl53l0x.html with datasheet.
Pololu VL53L0X : https://www.pololu.com/product/2490
Adafruit VL53L0X library : https://github.com/adafruit/Adafruit_VL53L0X
The .begin() function calls Wire.begin() to initialize the I2C bus and calls .setAddress() to set the address while that sensor is selected, as in the example vl53l0x_dual.ino
So when all three are connected, then the first one already fails which did not fail with only two sensors
Can you show a photo of the wiring ? Do you power the modules with 3.3V to VIN ? Have your removed the pullup resistors from the Due board ? Are they 1k5 or 1k ? Perhaps there is a bug in the library that makes it fail with Wire1.