I have the same problem with the 10.14.3 combo update, for me the problem did not start with Mojave or this update.
Since installing Mac OS High Sierra I have not been able to install any system updates.
The incremental system updates download fine from the App store then I press restart. The computer changes to the black screen with the white Apple and the the message installing update, the progress bar does not move, after a couple of minutes the Macbook restarts without installing the update and leaving a folder named macOS Install Data on my hard drive.
For every update I have tried the following:
- Restarting in Safe Mode to install.
- Reseting the NVRAM and the SMC.
- Reinstalling Mac OS from recovery partition and internet recover.
- Downloading combo updates.
- Running Disk First Aid from recovery partition.
- Enabling Root User to install.
Non of these actions have resolve the issue. The only method I have found to work is downloading the combo update on another Mac and then installing it on the Macbook Prom using target disk mode.
By the way I have this issue on two computers, an iMac 27 and a Macbook Pro, both are formatted as APFS drives.