This work presented the first thorough exploration of the attacks on the interface between gate-level and pulse-level quantum circuits and pulse-level quantum circuits themselves. Typically, quantum circuits and programs that execute on quantum computers, are defined using gate-level primitives. However, to improve the expressivity of quantum circuits and to allow better optimization, pulse-level circuits are now often used. The attacks presented in this work leverage the inconsistency between the gate-level description of the custom gate, and the actual, low-level pulse implementation of this gate. By manipulating the custom gate specification, this work proposes numerous attacks: qubit plunder, qubit block, qubit reorder, timing mismatch, frequency mismatch, phase mismatch, and waveform mismatch. This work demonstrates these attacks on the real quantum computer and simulator, and shows that most current software development kits are vulnerable to these new types of attacks. In the end, this work proposes a defense framework. The exploration of security and privacy issues of the rising pulse-level quantum circuits provides insight into the future development of secure quantum software development kits and quantum computer systems.