Very common for the Y on BPs to refer to the Y / Economy cabin and not the fare class. Very likely this was not a Y fare class ticket and was one on the discount fare classes on TAP that do not earn miles (A, E, F, I, N, O, P, R, T, X )

"Y" has multiple meanings / uses.

If you don't have any documentation of the actual fare class, you can try calling TAP and asking.