The teachers are the system. If female teachers, which make up the bulk of the educational workforce, are under-grading boys across the board, this is a systemic problem. It is not an isolated incident but a problem of discrimination playing out within the school system. 
If it was a case of individual teachers sometimes under-grading and sometimes over-grading boys, then the trend would not be visible in large sample sizes. The fact that the trend is visible means that our way of measuring performance inside the school system is inherently weighted against boys. By moving it more towards measuring objective skill, boys would be able to close the academic gap emerging between the sexes.