。
During sex she had a bored look on her face.
Literal
Intercourse [attributive-の] middle she [topic-は] boring-looking [attributive-な] face [object-を] was-doing-[continuous-ていた].
A striking register clash: 性交 is the clinical/formal term for 'sexual intercourse' (like English 'intercourse' or 'coitus'), while the rest of the sentence (つまらなそうな顔をしていた) is casual spoken Japanese. The ~そう evidential appearance suffix on つまらない gives 'looking bored' — attached to i-adjective stems it means 'appearing X.' ~の最中 'in the middle of X.' 顔をする is the idiom 'to have/make a face (expression).'