We find a new contribution in wave-packet scatterings, which has been overlooked in the standard formulation of S-matrix. As a concrete example, we consider a two-to-two scattering of light scalars ϕ by another intermediate heavy scalar Φ, in the Gaussian wave-packet formalism: ϕϕ→Φ→ϕϕ. This contribution can be interpreted as an “in-time- boundary effect” of Φ for the corresponding Φ→ϕϕ decay, proposed by Ishikawa et al., with a newly found modification that would cure the previously observed ultraviolet divergence. We show that such an effect can be understood as a Stokes phenomenon in an integral over complex energy plane: The number of relevant saddle points and Lefschetz thimbles (steepest descent paths) discretely changes depending on the configurations of initial and final states in the scattering.