An extremely low mower setting causes scalping of the lawn. Ideally you should remove no more than one-third the length of the grass blades with each mowing. Uneven ground can sometimes make this difficult to do. Areas where grass blades were cut too short will usually recover slowly, but the brown patches may be evidence that you cut into the crown (growing point) of some grass plants and killed them. 

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If the dead patches are no more than a few inches in diameter, grass regrowth may fill in the bare spots. Larger dead patches will need to be overseeded or resodded. Avoid fertilizing the grass now. That would further stress the roots. Wait, and let the grass recover on its own before feeding it. Be sure to water the lawn to prevent it from also suffering moisture stress.