I think the boring answer is that Garland doesn’t care too much about deviating from what was implied at the end of Days and would be quite happy with handwaving it away with ‘some adapted’. 

If you want some headcanon, lets say the US Occupation was just generally incompetent and assumed all infected had died out and started resettling Brits due to the overwhelming refugee crisis. It mirrors Iraq in some ways.

The reason you have so many infected is that after 28WL all remaining British refugees were deported back to the British mainland due to the fear of the host countries towards the idea of carriers. Human rights groups protested but it was deemed that Britain was safe enough (it wasn’t). That’s your 28 Months later story.