Ensure all pullups connected to AM335x are pulled up to the correct I/O voltage to avoid any leakage between the I/O rails of AM335x. Each terminal has an associated voltage used to power its I/O cell. This can be found in the AM335x data sheet, in the Ball Characteristics table under the "ZCE Power/ ZCZ Power" column.
For example, if you want to pull up terminal SPI0_CS0 in any mux mode (gpio0_5, i2c1_scl, and so forth), pull up the signal to VDDSHV6.