Apart from absences caused by farm jobs or helping out at home the other most common cause of small numbers at school was sickness. Serious epidemics of whooping cough, measles, smallpox, diptheria, and other occasionally deadly diseases were very frequent in Victorian schools.
The food and living conditions of many families were poor and illness often spread through the community very quickly, as in this 1897 example from Abergwesyn School...

This diary entry reads -
20th January - "There has been an outbreak of Diptheria in the village of Llangammarch, and as there has been one fatal case, a great many parents kept their children at home for fear of infection..."
Diptheria was a very common disease in Victorian times which led to severe inflammation of the throat. It was highly infectious, caused many deaths, and is fortunately now quite rare.
There is more about sickness and schools on the next page...

Death in the family, again...