Solution
As shown in the image below, this error is caused by trying to access the same method using different clock domains. In this case, the code is trying to access Mod1/DIO0 using an FPGA I/O Node from the default 40 MHz Onboard Clock (from the cRIO-9098 being used), and the derived 80 MHz clock:

To solve this you need to make sure all the calls to the same method are being made from the same clock domain. In the example shown, assuming you need to use the 80MHz derived clock, then you need to change the first two calls to Mod1/DIO0 to use the same clock domain using a Timed Loop:

This will clear the error message when trying to generate the intermediate files.