Laboratories around the world are producing plasmas with atomic population inversions that are exhibiting gain at wavelengths approaching the carbon K edge near 44 Å, which is optimal for holography of wet biological samples. Often these demonstrations of gain are accompanied by anomalies that may be due to atomic physics effects, but whose possible causes due to plasma physics effects are explored here. The optical pump laser’s pulse duration ranges from the relatively long (>1 nsec) to the ultrashort femtosecond regime, and its incident irradiance varies by many orders of magnitude as well. This broad range of results is analyzed here from a unified point of view, via the use of a suite of large simulation codes. The plasma gain media exhibit many laser–plasma instabilities, including stimulated Raman scattering (which is used to infer the evolution of an exploding foil x-ray laser target’s electron temperature and density), and possibly filamentation, radiative instability, and ion acoustic turbulence, all of whose resultant nonuniformities can seriously affect the x-ray laser beam’s propagation and achievable gain-length product. Non-Maxwellian distributions of electrons and nontrivial x-ray laser line shapes may also play a role in explaining some of these anomalies.