The fact anyone would think this is unfair or that 'naice' students should get some special pass confuses me.
I don't think it is unfair, but I do think it is counterproductive given what the school is presumably trying to achieve.
Why? Because somebody who is 15 (hence probably in Years 10 or 11), and has never got a behaviour point before, is probably pretty proud of that record. If the school had said - given your record, we won't give you a behaviour point this time, but next time we will, the student will likely double and triple their efforts never to forget to hand in homework, and I bet there will never be another occasion.
However, now that she has one - well the difference between one and three and, say, ten, probably is not that great - so the incentive to work triple hard to make sure one's record is not sullied has gone, and there is a reasonably high chance that there will be a second and a third. So if the school is really concerned about having homework handed in, then for students who have this kind of record, overlooking one infraction makes sense.
This is very different to the student in Year 7 who doesn't hand in their first or second or third piece of homework. Of course they will need to hand out the behaviour point, because otherwise the student will learn that there is no consequence to not handing in the homework, and it will provide an incentive to continue not to hand in the homework. But even there, if the same behaviour point is handed out for not handing in homework, and talking in class, and talking in the corridor, and having their top button undone, and having their shirt untucked, and a million other infractions, then the student will equate not handing in homework will all of the others - whereas not handing in homework, I suspect, is more directly important to learning and achievement than not tucking in one's shirt. How one runs the behaviour points scheme therefore can give students some pretty odd messages about the relative importance of various actions, and about what the school is trying to achieve.