Lack of experienced personnel. There was a choice between committing to the transport of men or the transport of cargo. The experienced escourts and crews went to the transport of soldiers to the British Isles, leaving the cargo ships with woefully inexperienced protection.
The other part is that the Wolf Pacts found easier prey outside the US than facing experienced RCN onslaughts. The Wolf Pacts were hounded out of Canadian waters and found American waters with easier prey.
RCN protection during the beginning of the war were just as inadequate as the USN during the Happy Times.