PCIe is packet-based and will retry, but typically the drivers for PCIe devices are not written to expect that e.g. accesses to its MMIO space take arbitrarily long times to complete, and the software above and around the driver (including the OS) can also be affected by such delays. Likewise, a device that's processing a continuous stream of data is going to overrun or underrun if its requests for interrupts or DMA get delayed due to retries caused by physical layer errors.