In this work, a multilayer security solution for digital communication systems is provided by considering the joint effects of physical-layer security channel codes with application-layer cryptography. We address two problems: first, the cryptanalysis of error-prone ciphertext; second, the design of a practical physical-layer security coding scheme. To our knowledge, the cryptographic attack model of the noisy-ciphertext attack is a novel concept. The more traditional assumption that the attacker has the ciphertext is generally assumed when performing cryptanalysis. However, with the ever-increasing amount of viable research in physical-layer security, it now becomes essential to perform the analysis when ciphertext is unreliable. We do so for the simple substitution cipher using an information-theoretic framework, and for stream ciphers by characterizing the success or failure of fast-correlation attacks when the ciphertext contains errors. We then present a practical coding scheme that can be used in conjunction with cryptography to ensure positive error rates in an eavesdropper's observed ciphertext, while guaranteeing error-free communications for legitimate receivers. Our codes are called stopping set codes, and provide a blanket of security that covers nearly all possible system configurations and channel parameters. The codes require a public authenticated feedback channel. The solutions to these two problems indicate the inherent strengthening of security that can be obtained by confusing an attacker about the ciphertext, and then give a practical method for providing the confusion. The aggregate result is a multilayer security solution for transmitting secret data that showcases security enhancements over standalone cryptography.