Ordered ships sometimes ignore the wormhole and deadhead.

[Deantwo]

The crew doesn't say on the Crew channel why they are deadheading instead? They will announce if it is because the wormhole is blocked.

There is a bug report about missing wormholes though, so it could be that. You will have to inspect the wormholes in each system along the route a little better.
See: (Bug report) wormhole scans innacurate