We are interfacing FT232 to aducm3029 which operates at 3V. But the FT232 operates at 3.3V . Will this cause a problem?
ADuCM3029 can work up to 3.6v supply voltage as per datasheet so powering the microcontroller with 3.3v is fine. Just don't exceed more than 3.6v supply voltage or it will damage the microcontroller.
The GPIOs have internal diodes for ESD protection. With a 0.3V difference even the diodes will not conduct, so you should have no problem interfacing the ADuCM3029 at 3V with the FT232 at 3.3V.