Depends on the level of automation. A ship with engines and reactors that run its own routine diagnostics, but require people to go and replace the power coupling when it goes bad sounds like it would be commonplace. It may even perform its own adjustments (as per the engineers input), but the manual knob-tiddling is still as an override option.
The navigator may just have to punch in to "go to Regina", and the ship does the necessary procedures to enter jump. But the people still are needed to tell the computer where to go.
Cargo bots may be there in place of a human in a Waldo, but they're just taking orders from the humans telling them to unload, and where to unload to.
Sure the automation may be smart, able to understand what a human what's it to do (put that *points at box* over here *points*), but I limit it to going off its script. You can't tell Siri to play angry birds for you, but you can tell her to open the app up. Or to open a walkthrough up for you and read it to you as you do it.