Yes, the FAA can do that. Usually it's routine.

May have been checking out the specific airplane or the specific airline, maybe checking out the pilots for compliance with procedures, maybe checking out the ATC procedures along the route, maybe monitoring the enroute navigation aids for functionality, maybe just going to OMA for some other unrelated purpose, or maybe ??? whatever.

Certain FAA employees ride in the cockpit as part of their job, so that's why they have to coordinate with the flight crew ahead of time. It's probably nothing to worry about.