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This is because Phi(33, Y) is still a polynomial in two variables:
sage: Phi(33, Y).parent()
Multivariate Polynomial Ring in X, Y over Finite Field of size 8009
So, you have to turn it into a one-variable polynomial first:
sage: S.<Y> = GF(8009)[]
sage: S(Phi(33, Y))
Y^3 + 6150*Y^2 + 5541*Y + 1175
sage: S(Phi(33, Y)).parent()
Univariate Polynomial Ring in Y over Finite Field of size 8009
sage: S(Phi(33, Y)).roots()
[(898, 1)]
