The Northwest Rebellion precipitated all manner of problems on Battleford's Principal. Even after Clarke and his charges were back in renovated facilities at the former Government House, the headmaster could not get the enrollment up to revised departmental expectations of thirty boys and thirty girls.

    It was becoming clear by later 1880s that Indian parents were turning against the Battleford School. Clarke reported the Indians as objecting 'that the boys have been kept longer than was agreed to keep them.' Amid charges of exploitation of the student body, other frequent complaints concerned diet and medical attention. Clarke attempted to deflect the blame for allegations of insufficient food onto an Indian Affairs official. To exacerbate Clarke's predicament, by 1890 he was coming under criticism and attack for his management of his staff and his lack of fiscal control.

    More generally, Indian Affairs officials found Clarke 'disposed to be dictatorial,' and his unpopularity caused as much trouble with the Indians from whom the school had to recruit students as it did with school staff.

    During a conversation with Clarke, the Anglican bishop of Saskatchewan and Calgary 'remonstrated with him about his habit of drinking to excess, of which I have heard for years, and he has promised to be more on his guard in future.'