NetFlow Analyzer shows interfaces as down when the interface in the network device monitored is administratively down.
The most common reason for an interface being administratively down is that someone has entered the shutdown command in interface config mode.
If the device is new and not yet configured, the interfaces will be administratively down.
In both the cases you have to manually enable the interface with "no shutdown" command.
NetFlow Analyzer checks whether the interface is down using SNMP. If SNMP credential is not associated or associated SNMP credential is wrong then only no flows alert will be generated as it is not possible to get the interface status without SNMP.
NetFlow Analyzer sends out no flow alert if there is no flow from the interfaces for more than 5 mins(Configurable).
There can be many reasons for no flows being received from the interfaces of a device.
The most common reason is the misconfiguration in the device where the route is not configured properly or if there is wrong access-list or QOS configured in the interface which is blocking the flows.
Please verify the configuration on the device to overcome this issue.