I've mentioned the wierdness with sources on Github but the problem seems to be more complex. A polygon with lowland meadow listed as the first habitat and coastal and floodplain grazing marsh listed as the second habitat comes out in the export with coastal and floodplain grazing marsh as the first habitat, a blank second habitat and lowland meadow as the third habitat.

In addition some first listed habitats come out as BAP habitat 1 and 3.