We study spurious second-order stationary points and local minima in a nonconvex low-rank formulation of sum-of-squares optimization on a real variety X. We reformulate the problem of finding a spurious local minimum in terms of syzygies of the underlying linear series, and also bring in topological tools to study this problem. When the variety X is of minimal degree, there exist spurious second-order stationary points if and only if both the dimension and the codimension of the variety are greater than one, answering a question by Legat, Yuan, and Parrilo. Moreover, for surfaces of minimal degree, we provide sufficient conditions to exclude points from being spurious local minima. In particular, all second-order stationary points associated with infinite Gram matrices on the Veronese surface, corresponding to ternary quartics, lie on the boundary and can be written as a binary quartic, up to a linear change of coordinates, complementing work by Scheiderer on decompositions of ternary quartics as a sum of three squares. For general varieties of higher degree, we give examples and characterizations of spurious second-order stationary points in the interior, together with a restricted path algorithm that avoids such points with controlled step sizes, and numerical experiment results illustrating the empirical successes on plane cubic curves and Veronese varieties.