Translation:You do not know if the cook has the fish.
Because "se" means "if". "Si" is a reflexive word that doesn't fit with the sentence.
I know what you mean. With me, it's Spanish. I took it for long enough that the Spanish pops into my head first. And Duolingo has no sense of humor when I do things like type "que" instead of "che"!
"Conoscere" means "to know" in the sense of being familiar with something and is often used with people. Conosci Mario (you know Mario / you're familiar with Mario).
"Sapere" means "to know" in the sense of knowing how to do something or knowing information/facts. In this case, we're talking about a piece of information (whether or not the cook has the fish), so we use sapere. Non sai se il cuoco ha il pesce (you don't know if the cook has the fish / you don't know the information about whether or not the cook has the fish).
Duolingo is programmed to automatically accept most contractions, including "don't" for "do not", so if it was marked wrong, you've either encountered a bug (https://support.duolingo.com/hc/en-us/articles/204728264-How-do-I-report-a-bug-), or you made another mistake in your answer that got it marked wrong.