Giving out two different colours of cards seems to generate extra work for the office staff, so there must be a reason for it.
Most likely, they have a set number of spaces for boys and girls, based on room sizes, so they can quickly and easily identify whether they have the right spaces available to allocate, especially if more than one person may be issuing the cards.
Imagine you are running a trip for a maximum of 32 children. On a day trip, you would allocate the spaces until you have 32 filled.
However, on a residential trip the children have to sleep in single sex rooms, so you decide to allocate 16 boy spaces and 16 girl spaces. It would not be possible to accept a 17th boy or girl on the trip, as there would not be a bed in the right room, even though there would be an available seat on the coach.
In a busy school office, by allocating colours, it would be easier to see that you have so many boy-spaces and so many girl-spaces available so you don't inadvertently accept a child that you can't allocate a bed to.
The school could have chosen a different colour-coding system, but it would still mean colour A = girls and colour B = boys.
No system is perfect. Perhaps we should wait for the thread that begins, "I was late returning the form for my child's residential trip and now they can't go because they are a boy, but my friend's daughter has been given a space."