That parenthetical is an important and almost always unstated axiom.
The general inability to prove a false statement does not mean you cannot prove that the answer to some equation is a number below zero. I am not really aware of the phrase being used in the context of math, but rather more often with examinations or experiments that are susceptible to evidence.
To be sure, "you cannot prove a negative" is itself unproven. It more a rule of thumb to remind you not to assume that though some statement is false now that it always was false and always will be false.
It's not perfect, but it's also not a law of logic or anything. It's just a guideline.
On a side note Fermat's Last Theorem isn't a good counterexample because it hasn't been proven yet either.
Both in math and in the real world we don't have 'perfect observation'. There is plenty of conjectures in math and the real world that lack a proof of something being true or false.
I think "can't prove a negative" is one of the least informative ways of trying to say something, I assume he meant to say "absence of evidence is not evidence of absence" or perhaps "absence and evidence don't commute"