In this case, the change agreed to between the Department of Canadian Heritage and the department concerned takes precedence over other regulations under the Fisheries Act, the Coastal Fisheries Protection Act, the Canada Shipping Act, the Arctic Waters Pollution Prevention Act, the Navigable Waters Protection Act or the Aeronautics Act.
The Department of Canadian Heritage cannot disagree with the Coastal Fisheries Protection Act
The statement says that an agreement with this department has taken precedence over this act, indicating the two must disagree in some manner.  I am not sure why the model cannot predict this one.
( z0 possible :ARG1 ( z1 disagree :ARG0 ( z2 government-organization :name ( z3 name :op "Department" :op "of" :op "Canadian" :op "Heritage" ) ) :ARG1 ( z4 law :name ( z5 name :op "Coastal" :op "Fisheries" :op "Protection" :op "Act" ) ) ) :polarity - )
(z0 / possible-01
    :ARG1 (z1 / disagree-01
              :ARG0 (z2 / government-organization
                        :name (z3 / name
                                  :op1 "Department"
                                  :op2 "of"
                                  :op3 "Canadian"
                                  :op4 "Heritage"))
              :ARG1 (z4 / law
                        :name (z5 / name
                                  :op1 "Coastal"
                                  :op2 "Fisheries"
                                  :op3 "Protection"
                                  :op4 "Act")))
    :polarity -)
The Department of Canadian Heritage cannot disagree with the Coastal Fisheries Protection Act
z2 :name z3
z3 :op1 4
z3 :op2 8
z3 :op3 2
z3 :op4 6
z0 :polarity 0
z0 :ARG1 z1
z1 :ARG0 z2
z1 :ARG1 z4
z4 :name z5
z5 :op3 7
z5 :op2 5
z5 :op1 3
z5 :op4 1