She must have declined more rapidly than expected. Even near the end, it's very difficult to predict death accurately - which is one reason why HCPs are usually reluctant to be too definitive - we have all been proven wrong too many times. And sometimes older people can seem to be at the point of no return, and then bounce back. I remember, as a junior doctor, telling my consultant that I thought a patient was about to die, and we needed to call her family. We went to her bedside - only to find she had got out of bed and was happily eating toast.
So I think something happened on Wednesday that was serious. The way the cancellation of the Privy Council was reported was weird - the media put a lot of emphasis on it, even though the Queen had cancelled many other events over the last few months without it being a big deal. So I'm guessing the media were briefed that this might be the beginning of the end. However I assume her doctors didn't think she was dying imminently, as they didn't send for the family.
Even on Thursday morning, she presumably was not too bad as only Charles was sent for, initially. Then she must have taken a turn for the worse, and died more quickly than anticipated.
I don't want to speculate on what she actually died of, but there are many conditions that affect elderly people that could fit this pattern, including (just as an example) heart failure.