Haven't we already developed the technologies for manned missions?
But we don't even need to look at such exotic possibilities as an alien ship.
Then why did you mention it?
You have a deep fissure in the asteroid,
Do asteroids have deep fissures, and if they do would NASA risk sending an astronaut into it?
A human would dig as deep as practical, climbing down into the hole as needed or making an extension for the shovel out of spare parts and duct tape. A robot can't dig deeper than its mechanical arm is, end of story.
How deep did the astronauts dig on the Moon?
A human would take a hammer and split the rock in two, and the answer is immediately obvious.
Why can't the machine return the rocks to Earth to be studied?
No. I went outside and looked up, and I couldn't see any interplanetary spaceship in orbit, ready for a mission.
But we don't even need to look at such exotic possibilities as an alien ship. -- Then why did you mention it?
Because it's fun, of course. And because it may happen. Many SciFi writers speculate that humanity will get the next scientific breakthrough from an alien civilization. Or we can build our own FTL drive, it will take only a few thousand years; our knowledge of this Universe is very spotty at the moment. As an example, we don't know what causes such a mundane thing as mass.
Do asteroids have deep fissures, and if they do would NASA risk sending an astronaut into it?
They may have them. If they do it's up to the astronauts to decide if the descent would be safe enough. For example, you can descend into the Grand Canyon without fear that it will close upon you. And you can't fall on an asteroid.
How deep did the astronauts dig on the Moon?
"The Apollo moon rocks were collected using a variety of tools, including hammers, rakes, scoops, tongs, and core tubes." (link).
Why can't the machine return the rocks to Earth to be studied?
It would be a shame to return a wrong rock. A geologist at the site would instantly decide what should and what shouldn't be returned. Most interesting rocks are not on surface anyway, that's why I mentioned fissures.