I ran into this problem with an external time machine drive and another external hard drive, both formatted as AFPS. I wrote a startup script following these steps to address the problem:
1) plug in your external hard drive and mount with the Disk Utility app (under Applications / Utilities) by selecting the drive from the list in the left side and clicking the Mount icon
2) open Terminal (under Applications / Utilities), type in "diskutil coreStorage list" and press enter
3) each APFS volume will have 4 entries, the first is a "Logical Volume Group", then a "Physical Volume", then a "Logical Volume Family", and finally a "Logical Volume". Copy the identifier following "Logical Volume", it's in the following format (where X can be a number or a letter) XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
4) open the Script Editor App (under Applications/Utilities) and click "New Document" or simply press Cmd + N
5) for each APFS drive you want to mount on startup, enter the following, using the volume identifier copied in step 3:
delay 15
do shell script "diskutil coreStorage unlockVolume XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX -passphrase [volume password]"
[Note] to unlock multiple volumes, simply add " && " followed the above command (using the volume identifier from the second hard drive in step 3):
delay 15
do shell script "diskutil coreStorage unlockVolume XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX -passphrase [volume password] && diskutil coreStorage unlockVolume XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX -passphrase [volume password]"
6) save the script somewhere, then select File / Export; under "File Format" select "Application"; leave everything else blank and save the application somewhere
7) open the System Preferences app (click on the apple menu at the top left of your taskbar), then click on Users & Groups; select your user, then click on the Login Items tab; drag the application you saved in step 6 into the list
8) when you restart your computer, your hard drives should be automatically unlocked and mounted
Whenever apple comes out with another update, I would remove the script from your startup items and see if the issue has been fixed. If not, this should continue to work until Apple resolves the issue.