It is always easier for us when we have access to your project. Can you please post your complete project so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
As it is a warning, it will still compile without changing it;
Most likely, it is warning you since the RTC generates it's own ISR for handling the WDT2 interrupt (my guess anyways), thus the compiler is warning you that things might not work if you don't let the compiler generate the ISR from the WDT for usage by the associated (RTC) component.