First of all - i'm writing this here and not as an email or a private message, because it's a problem that more than one of us had in their homework, and I believe that the course's staff response is relevant for everybody.
In question 5, many of us identified the end of a string using the char "]".
It matches all the cases in all the .txt files, and it fits the first example given in the question:
">gi|229508971|ref|ZP_04398461.1| sulfur carrier protein adenylyltransferase ThiF [Vibrio cholerae B33]
as for the second example, it was written as:
So it doesn't contradict this as well… the "…" in this example meant for us: "It continues Just like all the others…", meaning it included "]" just like them…
I talked to Ofir Chen about this, and he did not give me a satisfying response.