We study a new transistor-level side-channel leakage caused by charges trapped in between stacked transistors namely residual electric charges (RECs). Building leakage models is important in designing countermeasures against side-channel attacks (SCAs). The conventional work showed that even a transistor-level leakage is measurable with a local electromagnetic measurement. One example is the current-path leak [1], [2]: an attacker can distinguish the number of transistors in the current path activated during a signal transition. Addressing this issue, Sugawara et al. proposed to use a mirror circuit that has the same number of transistors on its possible current paths. We show that this countermeasure is insufficient by showing a new transistor-level leakage, caused by RECs, not covered in the previous work. RECs can carry the history of the gate's state over multiple clock cycles and changes the gate's electrical behavior. We experimentally verify that RECs cause exploitable side-channel leakage. We also propose a countermeasure against REC leaks and designed advanced encryption standard-128 (AES-128) circuits using IO-masked dual-rail read-only memory with a 180-nm complementary metal-oxide-semiconductor (CMOS) process. We compared the resilience of our AES-128 circuits against EMA attacks with and without our countermeasure and investigated an RECs' effect on physically unclonable functions (PUFs). We further extend RECs to physically unclonable function. We demonstrate that RECs affect the performance of arbiter and ring-oscillator PUFs through experiments using our custom chips fabricated with 180- and 40-nm CMOS processes*.