I have a similar issue only it's worse for me. seems to be if an unarmed survey ship has previously been defeated by pirates, any time I revisit that anomaly (either manually or automatically) I get the same issue. Idle ship greyed out in bottom right and game does not progress.
If it's an unvisited anomaly then I often (but not always) get the hang when auto exploring, but can usually restore an autosave and visit manually successfully
This is using the opt-in Beta on steam