Why do faith schools sometimes ignore teaching about homosexuality or contraception?

Because they go against their religious beliefs. For example, homosexuality is condemned in the Torah/Bible (Leviticus 19:22) or the Quran (15th surah, verse 74). You can find similar bans on contraception (e.g. the sin of Onan, Genesis 38:9-10). So some religious schools believe in teaching according to government guidelines they're going against their religion, and also imperilling the souls of their students.

They are also however breaking the law. A faith school that refuses to teach on these subjects in accordance with government guidelines would be in for a tough time when OFSTED calls.