I have a Mac Mini (late 2014) with its stock internal drive and an external SSD via USB. The external drive has Sierra and this is what I always boot from. The internal is a clone of the external just for backup, cloned via SuperDuper.
According to https://support.apple.com/en-us/HT210190 I can update directly to Mojave on this Mac Mini. I downloaded the installer from the App Store and ran it to install on the external drive. It took about 25 minutes and gave a "success" message, prompting me to restart to finish. When I restarted, it booted from the internal drive instead. I went to the Startup Disk pref pane and made sure the external was selected and tried again. It booted again from the internal drive. Good thing I had it as a backup 🙂
In the Startup Disk pref pane, the external drive is selectable but it still shows as a Sierra boot. I can tell the install did write to the external drive but I suppose it didn't finish. I ran the installer again — it only took a few minutes and again showed "success" and a restart prompt. Same result.
Before I take the time to wipe the external drive and try a clean install (then restore all my stuff), anyone know what's going on?