Software defines digital infrastructures in the manufacturing industry, connecting services and computation resources to machines and devices. These infrastructures aim at increased flexibility, scalability, and a wider application portfolio for automated manufacturing processes. At the same time, the complexity of securing software increases dramatically. Threats to confidentiality, integrity, and availability of software can result in critical losses for automated industrial production and impact manufacturing companies. In order to map existing and emerging security challenges, we present the results of a hermeneutic literature review structured along abstraction levels and vertical integration of software. Based on this structure, we derive implications for academia and practice focused on system integrators, developers, and security auditors of digital infrastructures. Thereby, we discuss courses of action mapped to software security black boxes, infrastructure heterogeneity, and the adaptation of security for operational usage.