No, the "allegedly" is that they did it deliberately. They definitely put this woman on the No-Fly list; she's demonstrably on it. The question and concern is over whether they did it in order to hinder her testifying in this case.
No, whether or not she is actually on the no-fly list is not considered fact yet. It is possible she could have lied and faked a document. I do not think she did that, and it appears nor does the judge, but the judge wants more evidence to support the claim. From the article:
But Judge Alsup noted that the document with the DHS instructions to the airline was not supported by any sworn testimony or evidence of its authenticity. “You have to have a sworn record before I can do something dramatic.” Judge Alsup said he would consider the document if and when Ms. Mustafa Kamal arrives in San Francisco and can testify as to its authenticity.
...
Judge Alsup wasn’t willing to take any action today on unproven allegations or unverified documents. But he made clear that, “I am disturbed by this…. We’ll hear from her [Ms. Mustafa Kamal] when she gets here. If it turns out that the DHS has sabotaged a witness, that will go against the government’s case. I want a witness from Homeland Security who can testify to what has happened. You find a witness and get them here.”
