Would this mean "the science lesson is good" or "the subject of science is good"?
The subject. If we were talking about a specific lesson, we would say kipindi.
"The science subject is good" is awkward English at best. It should be "the subject of science" or "the study of science". The phrase "science subject(s)" can occur in other contexts, e.g. "Physics and chemistry are important science subjects usually introduced in high school."
Duo should accept "the subject of science" and "the study of science" as correct answers.