This letter aims at analyzing subpixel misregistration between multispectral images acquired by the Multi Spectral Instrument (MSI) aboard Sentinel-2A remote sensing satellite, and exploring its potential for moving target and cloud detection. By virtue of its hardware design, MSI’s detectors exhibit a parallax angle that leads to subpixel shifts that are corrected with special preprocessing routines. However, these routines do not correct shifts for moving and/or high-altitude objects. In this letter, we apply a phase correlation approach to detect subpixel shifts between B2 (blue), B3 (green), and B4 (red) Sentinel-2A/MSI images. We show that shifts of more than 1.1 pixels can be observed for moving targets, such as airplanes and clouds, and can be used for cloud detection. We demonstrate that the proposed approach can detect clouds that are not identified in the built-in cloud mask provided within the Sentinel-2A Level-1C product.