Does anyone know if there is a software issue with using MQTT communication and I2C communication with the MKR series?
The issue is most probably in your code. Post it (don't forget the code tags!) and post links to the used libraries. Also post links to the used hardware as well as links to the schematics of the used breakout boards.
Please see the link below talking about ECCX08 chip and the I2C bus:
The ECCX08 chip uses the I2C bus and so once it is activated we are no longer able to access the I2C bus.
I found I need to do a Wire.begin(); before I call my I2C sensors again.