I assume you were flying OS.
Aeroplan's accumulation amounts varies for different OS fare classes:
Y, B 100% of miles flown (minimum 500)
M, H, Q, G, V 70% of miles flown (minimum 500)
W, S 50% of miles flown (minimum 500)
Sounds like you had a segment in M,H,Q,G,V class.
I'd check your ticket/receipt and contact AE if that segment was in Y or B.