Couples who want children don't necessarily have to produce them themselves. (Elton John and David Furnish have two sons, for example).
Sometimes transgender couples haven't actually had anything 'done to their bits'. So that the 'father', who was born a woman, can still give birth, as here:
http://www.bbc.co.uk/news/magazine-37408298
If you look under 'Transgender pregnancy' in that link though, you'll see this (which offers one possible answer to your question):
"Trans men, assigned female at birth, often receive hormone therapy treatment, but recent studies show that this does not prevent pregnancies in the short or long-term"
However this statement is also present there, which suggests that 'test-tube babies' might be involved:
"In the UK, the NHS funds sex changes for transgender people and offers them fertility treatment and the ability to freeze their egg and sperm"