This page describes various diagnostics produced by the networking and the PCI code that can be safely ignored.
The dp8390 driver got a message about an expired timer. But the driver does not use any timers. This is probably a small bug in the timer library. The message can be safely ignored (but it is better to fix the library).
Another harmless diagnostic. At the moment the information provided by the ISA bridge is not needed.
Either QEMU does not emulate the hardware correctly or there is a bug in the MINIX 3 PCI code. This error will be ignored for QEMU.
Some driver uses the general copy method rather than safecopy. The request is performed and everything should work normally, but the driver will need to be modernized at some point in the future.