Why in the prologue people are astonished by "floating rocks"? Why do they point it out?

It's described as a dark energy cloud, but does not behave in such a way that it's fully understood, and the fact that it disrupts instruments is what makes it difficult to scan.

I'm looking at the lore here and why things should or should not work according to it. Science says it shouldn't be possible. Fine. But the story says otherwise. So do we explain the lore by the science it contradicts when it's convenient to do so? Or do we take the lore for what it is and expect some kind of continuity from it? I say we do the latter.

You don’t need to know what it is, the scanners should have picked some kind of anomaly and avoided the cloud.

Anything that is not ordinary and cannot be scanned correctly should have been avoided by the AI controlling the ship.

Also if one ship runs in to trouble they would have left some kind of beacon for other ships following to avoid the problem.

These are all standard procedures so enough with the excuses that a 10 year old can figure out.

You don't need to pinpoint it just avoid it and a 10 year old would do a better job than the Bioware writers.
And again there was no beacon for anyone following to avoid.
I mean it is obvious that no other ship would want to help their friends following behind and would prefer that they all die.

The warp of communications alone should stop the ship to take a different direction.
They would have had more than one scanner on the ships to scan for different things.
We are not dealing with idiots but with people who travel for over 600 years and who should have found much bigger problems on the way to the destination.
And what about some help from ships that have traveled before us?
Were we not going to leave a message for ships that would come after us if we did not fix the problem?

Why would they have found bigger problems in utterly empty space? 

I don't see how the scanner argument can go anywhere. Making a case that the Hyperion should have had sensors which were able to detect this phenomenon at sufficient range to prevent the accident would require a degree of technical knowledge that we don't have and probably can't have, since the MEU uses fantasy physics.

you don't understand. How can you avoid it if you don't know where it is? These sensor are their eyes.people don't direct space ship by look out a window. They use sensor to indicate where thing are and close they are to it. Flying in the scurge is like someone diving a car with a bright light in there face. Now image that person suddenly put in high speeds in to heavy traffic while being blinded by that light.

That's what it like to deal with the scurge. It's not something.you can avoid unless you know about before hand. Their sensors are messed up so they don't know where it is. It moves around them so where they cam from gets closed off. And it's constantly moving towards the ship because it's attracted to the drive core.
It space quick sand.

it's not empty space around the scorge. It's giant dark energy cloud to surrounds and are attracted to ships. It moves.

no it's not. You would need to have a reason to send the probes in. None one on the ship would had any reason to think that there was any danger in that system. Why would they think to a send probes in a place they don't think is dangerous. It like saying a person could easily avoid a mud slide if they stop and surveyed the area with a telescope while ignoring the person is given no indication the area is dangerous. The reason they hit the scourge is that they when into the system thinking everything was safe and by the time the ship sensors indicated anything was wrong they were already serounded by the scorge.

you're not getting. The range of the scanners are the range of the scourge. This is something so big it can cover the cluster. It fills systems and serounded planets. It so big it can hide Aya from the kett for decades. If the ship is in range of the scanners to sense distortion it's already too late, the scorge has already started to seround the ship and is already being attracted to the ship. The only real safe distance from the scorge is out side scanning range. Only pilots trained to fly around.the scourge can go though it safely.

That sounds like "Lithia", an episode of the Outer Limits that aired in 1998. 

I have explained it to you but if you do not want to understand that is your problem.