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Use OS X Combo Update instead of letting App Store Update option
Update means point release to a major software version and is different from Upgrading. See this article ➡︎
Combo Update means this update package contains all the point releases up to this point, i.e., OS X10.12.4 Combo Update includes files for OS X10.12.1、S X10.12.2、OS X10.12.3.
By running Combo Update, it will assure all the point release files will be replaced, which increases the chance of replacing corrupted files if any. This will not happen if you run Update from App Store under Menu. Google Combo Update to download as shown below:
Note: By its nature, there is no Combo Update for OS X10.12 → OS X10.12.1. However, obtaining the Update package from Apple Support site is still highly recommended. Just google the download link. There could be some bad interruption when updating App Store under Menu due to bad internet connection, which may or may not produce unreliable OS state down the load.