When making decisions in a cluttered world, humans and other animals often have to hold multiple items in memory at once – such as the different items on a shopping list. Psychophysical experiments in humans and other animals have shown remembered stimuli can sometimes become confused, with participants reporting chimeric stimuli composed of features from different stimuli. In particular, subjects will often make “swap errors” where they misattribute a feature from one object as belonging to another object. While swap errors have been described behaviorally, their neural mechanisms are unknown. Here, we elucidate these neural mechanisms through trial-by-trial analysis of neural population recordings from posterior and frontal brain regions while monkeys perform two multi-stimulus working memory tasks. In these tasks, monkeys were cued to report the color of an item that either was previously shown at a corresponding location (requiring selection from working memory) or will be shown at the corresponding location (requiring attention to a position). Animals made swap errors in both tasks. In the neural data, we find evidence that the neural correlates of swap errors emerged when correctly remembered information is selected incorrectly from working memory. This led to a representation of the distractor color as if it were the target color, underlying the eventual swap error. We did not find consistent evidence that swap errors arose from misinterpretation of the cue or errors during encoding or storage in working memory. These results suggest an alternative to established views on the neural origins of swap errors, and highlight selection from and manipulation in working memory as crucial – yet surprisingly brittle – neural processes.