Do you have the I2C pull-ups connected to the correct voltage? I2C interfaces require a pull-up resistor on both the data and the clock lines. 4.7K-Ω pull-up resistors must be attached on both I2C signals (x_SDA and x_SCL). Ensure the pull-up resistors connect to the correct I/O voltage rail. For more information, see the note on the Pull-up Resistors bullet in Section 2.7.
Are you using TI's software (Linux SDK) for PMIC control? The TI software expects the WKUP_I2C0 to be connected to the PMIC.
Do you need a fully compliant I2C buffer? The WKUP_I2C0 and MCU_I2C0 use true open-drain buffers that are fully compliant to the I2C specifications. These support 100-kHz and 400-kHz operation. The remaining I2C interfaces, I2C0-I2C2, use LVCMOS to emulate an open-drain buffer. These can support 3.4-Mbps I2C operations; however, these ports are not fully compliant with the I2C specification, in particular falling edges are too fast (< 2 ns). Any devices connected to these ports must be able to function properly with the faster fall time.