Many things can be misconfigured on an interface to cause it to go down.
This will cause a loss of connectivity with attached network segments. Changing
the subnet of an interface to a different one from the directly attached
network segment is an obvious way to shut down their connection, but this is
not a physical layer problem.
If a LAN segment has multiple links to the
network core, modifying the bandwidth parameter in a routing protocol could
also cause a router to favor alternate routes over the local link, resulting in
suboptimal network performance.
Other misconfigurations which are directly related to the physical layer
are:

- Serial links re-configured as asynchronous instead of synchronous
- Incorrect clock rate
- Incorrect clock source
- Interface shutdown
Switchport duplex configuration mismatches can cause collisions or port
shutdown to occur. Although the current state of auto-negotiation can often
negate this type of problem, at least one of the attached devices needs to be
capable of link speed and duplex negotiation.