It will result in unexpected PCIe® packet on the TX interface, such as ECRC error, illegal type of FmtType field and unable to accept further requests, if you use the original ICM example design generated by MegaWizard™, and application layer user logic sends MSI request to ICM module (Descriptor/Data Interface) coinciding with PCIe TX packet.
To prevent this problem, the application layer user logic must have exclusive control of MSI request and TX packet. MSI request must NOT be sent to ICM coinciding with TX packet.
When the descriptor/data IP Compiler for PCI Express is generated, the example designs are generated with an Incremental Compile Module (ICM). This module facilitates timing closure using Quartus II incremental compilation and is provided for backward compatibility only. The ICM facilitates incremental compilation by providing a fully registered interface between the user application and the PCI Express transaction layer.