What to do with threats of blacklisting? To be brief, I am a PhD student in the UK, and I have recently had some disagreement with the way my advisor handled our collaboration on research. This was initially a fairly minor thing. Not in the sense of what has happened, but minor in the sense that I only wanted to move past it, and to continue productively, but unfortunately he appeared to be too preoccupied, or for whatever reason, unable or unwilling to work together on correcting our results. Frustrating and not good for me, but ok, fine. At the time, no harsh words were exchanged at all, and there was some degree of understanding, although I was not happy with the mistake.

This has escalated beyond belief as soon as I relayed this problem to an administrative person, to explain there was a mutual mistake and I needed more time to submit. I explained the situation briefly to the person responsible for these things, made it clear I held no animosity or any interest in dwelling on it, and just needed some recovery time to move forwards. This was made totally clear to him and he was fine to shift the submission date and funding termination back slightly and he had agreed with me that there should be no blame here.

This has resulted in my advisor going on a furious rant at me in public, saying he refuses to work with me anymore. In private, the advisors have said that my 'complaints' have made the group look bad (no complaint was ever made, only a request for further time), and that they have now lodged some files or something on me with people at the university marking me as problematic. I have also been told that my complaints will make it difficult for me to get a job even after graduation, if I get to that point, because my advisor has no intention of giving me a reference, much less a positive one, and that they can make finding a job very difficult.

What on earth can I do? It seems that my career is now in ruins before it even started.

This whole situation has made me disgusted since it appears to have come almost out of nowhere, based on one conversation with an admin person. But I cannot work elsewhere if they follow through on their threats. How can I salvage my potential career?

Edit: There are just too many details I left out to edit down to size, and I would like to simply close this question or delete it if possible, due to confusion. I would prefer this to editing a popular question with too many specifics.
You went to the administrative person. That was your error and the core issue. 

Allow me to give an example from the other side in which this happened:

While I was at another institute, I was asked to take over a lab for another person. The lab hosted a guest cohort from another country so the university needed someone with content knowledge and dual language fluency on short notice. So I was asked if I could take over the lab for a week. 

Suffice to say, I did not know that there were particular rules for this lab. Some were obvious (like not leaving equipment plugged in) but I was a little overwhelmed with taking over a course last minute. Further, my work is primarily computational rather than lab focused so the reflex nature of lab rules was not there for me. 

After a few nights, the lab manager came in and saw the lab after I had left it. Equipment was left out and plugged in. All a very big mistake on my part. The way she responded was where things got messy. 

In hindsight, a more measured response would have been talking to me or even the lab's PI to find out what was going; even going to the department head. Instead she went to the Dean. She did not know the situation with the lab and the dean didnt, but as soon as it went to the dean, the situation became "administrative". Funds were threatened and it ended with me having to write a formal apology to the department head and the lab manager with everyone CCed on the email.  Everyone was aware the situation and most parties were mainly pleased that I was willing to write the apology so the "administrative" side of the situation could go away and we could fix things in house. (I ended up just getting an assistant who was a little more lab savvy). The department head came by and gave me a sympathetic pat on the back. 

Was I wrong, certainly. But it was likely an issue that could have been dealt with "in house". 

So, what was the end result of going to the administration rather than keeping things in house?  At one end, awkward elevator rides when the lab manager and I crossed paths. She found out the situation, and to find out, she didnt even know I was in the lab. I heard she thought it was an undergraduate group. On the other end, it did leave some lasting trust issues and undermined what had been before a very good working relationship between two labs. But I think that things have smoothed out since that happened. 

In other words, once you go to the administration, the situation becomes administrative.