You are absolutely correct that "calories" is plural subject and it does not agree in number with the singular verb "does not count". This is exactly what the question in Pre-assessment quiz for our Sentence Structure live session intended to check. Please see the screenshot below for the question. I believe you may not have read the question correctly
. This question was in fact designed to check whether you understand how to break the sentence into its clauses and whether you understand how to identify SV pairs. And it seems that you were definitely able to do that just right!
If you have any further questions about this, please feel free to post them in e-GMAT
internal forums. We have a very active forum at e-GMAT