I think you have an interesting concept here, it's thought out with a narrative and a clear emotion and intended impact on readers set out. That being said, let's break it down a bit.
For 100s of years the clones of an 8 year old boy has walked from a cave network in eastern Europe.
So this is something that's been going on for hundreds of years. Do they know that? Has the Foundation been tracking this anomaly from the start? Otherwise, how do they know that it has been going on for this length of time?
None of the children found have lived for more than a year.
Where did the children live? And did they just pop out as eight year old boys? The actual anomaly has a few logistics issues to me. They're all clones of this one person, so is the original one the one that grows up? Does he stay a kid? Does he die within a year, or just stay alive as a kid? Also, how did the Foundation find this anomaly?
All except for one instance, which is now isolated in a containment facility,
So they bring him to a seperate containment facility, what do they do with the rest of the clones? Also, does Daryl have any other anomalous properties? Speaking of him though,
The man, now 28, was named ‘Daryl’ by researchers.
The Foundation would not name an anomaly, even a humanoid. When humanoid anomalies have actual names which is most of the time, they don't call them by their name. They call them by their SCP designation. So why would they give him a name they wouldn't use? Why not just tell him his name is SCP-XXXX for simplicity?
From the start he claimed that he had no memory or knowledge of where he came from,
I could be wrong here, but I'm sure the Foundation would have some way of finding out the truth from him. I'm sure they could hypnotize him or do something to get the truth to come out.
that the clones are part of a project intended to colonise an unknown location.
This seems to be your main sort of narrative. While it's interesting, it has its problems. Daryl started out just like all the other clones, so did all of those clones know about the colonise project thing? If not, how does he know about it? And why is he manipulating the Foundation? Maybe that mystery is part of what you're going for, but right now it kind of just seems confusing. There appears to be no reason that he's dragging them along. Aren't they tracking the clones? And if they're not, how do they know about him?
Our first log will introduce a 16 year old Daryl who requests to meet one of his clones.
You said he was 28, so I guess you're taking a step back. I suppose this document would show research over the line of years?
The Researchers hope that this may lead to a breakthrough.
Why would allowing him to meet a clone lead to answers of any sort? What are they hoping to accomplish?
Instead Daryl murders the clone in a fit of rage.
In my opinion, I don't think he would have the chance to. There would probably be guards and as soon as they realize his intentions, they would stop him. You haven't mentioned any additional powers, and they definitely wouldn't allow anything that could be used as a weapon, so I guess he would go for strangling or bashing his head in—even so, I feel like the Foundation could intervene before things get too serious.
While not admitting so to the Foundation he simply wished to take out his frustration with the current failure of the mission on the one he blames; himself.
So is he the original or something? You didn't note this before.
Overall, I feel like you have an interesting concept, but it has a lot of logistic issues. I won't repeat all I said above, but I would suggest taking into consideration, and reworking your idea to make a little more sense. I'm not a huge fan of this personally, but it does have the potential to go somewhere.
Hope I could help! Good luck!