If an IP core is created in or regenerated through Project Navigator, the functional model and other supporting HDL files are generated for both HDL languages. For IP cores which generate an example design, some of the file names are the same in the "simulation" folder regardless of the language generated, so files are overwritten and do not work if it is not for the first language generated.
This issue affects MIG, Endpoint Block for PCI Express Core, Serial Rapid I/O, and some networking cores which generate an example design.