Hello,
Your problem is that you are connecting three I2C devices with identical device address on the same I2C bus.
So, when you send an I2C command to one ST25DV-I2C, they are in fact all accessed by this command.
It not possible to configure the I2C device address of the ST25DV-I2C, so normally, it should not be possible to connect three ST25DV-I2C on the same I2C bus.
One solution is to have 3 different I2C buses, and connect 1 ST25DV on each.
If you have only one I2C bus (this is your case), there is another possibility: you will need to put the two ST25DV-I2C that are not accessed in Low Power Mode when accessing the third one.
The good thing is that the X-Nucleo-NFC04A1 is using the 12 pins package version of the ST25DV-I2C. On this version, you have access to the LPD (Low Power Mode) of the device.
If you set the LPD pin to high, the ST25DV-I2C will enter the Low Power Mode. In this mode, it will answer normally to any RF request, but will not answer to any I2C command.
So, by setting high the LPD pin of two ST25DV, you can access the third one by I2C.
Of course, you will need little rework of the board. The LPD pin can be disconnected from the main nucleo board by removing the R11 resistor. You then need to reassign and reconnect this LPD pin of each ST25DV to another STM32 GPIO.
On the RF side, it is perfectly possible to have the 3 devices working together. This is by design supported by ISO15693 device. You need to access each device in "addressed mode", or use selected state to ensure you are talking to only one tag at a time.
Hope this help.
Best regards.