Trapped ions are one of the most promising platforms for quantum computing due to the longest qubit coherence times and the highest gate fidelities. However, scaling the number of ions (qubits) in a linear Coulomb crystal is the key difficulty on the way to multi-qubit systems. One of the promising pathways to scale the number of qubits is to implement the pulsed non-adiabatic gates based on the sequence of State Dependent Kicks (SDKs). We have analytically and numerically studied the influence of coherent effects in the SDK sequence and, correspondingly, have deduced the influence of the individual SDK error on the net gate fidelity. We have shown that the coherence effects significantly impact the fidelity of non-adiabatic gates and must be taken into the account. As practical examples, we have developed a numerical model for full simulation of coherence effects using a linear ion microtrap array and a 2D microtrap array. We have also studied the dependency of the gate fidelity on the laser power fluctuations.