I have been maintaining and developing a touchscreen system on an RPi 3B using Jessie Lite and, more recently, Stretch Lite that controls and encodes video for a Digital TV Transmitter. Full code here: https://github.com/davecrump/portsdown
I have touchscreen controlled functions for reboot and shutdown which simply terminate the running C code nicely and then issue the system command "sudo reboot now" or "sudo shutdown now" as appropriate. These work perfectly in the Jessie Lite version, but not in the Stretch lite version.
When I try to reboot or shutdown in Stretch Lite (2018-03-13 or 2018-06-27) the reboot or shutdown nearly always hangs at "Reached target shutdown". I can reduce the occurrence of this down to 1 in 5 by issuing the command "sudo swapoff -a" before attempting to shutdown, but this is not a totally effective cure. The likelihood of occurrence appears to be related to what the RPi has had to run since boot-up.
I realise that the next step is to turn on the systemd debug shell, (as discussed in this similar unsolved post viewtopic.php?p=1171303) but before I go on, I wondered if anyone had seen and solved this issue before.
It never happens with Jessie Lite, only with Stretch Lite; the install on both systems has only very minor differences. When it hangs, the RPi's power consumption increases as though it is working very hard. For this testing, I have no peripherals connected, only network for SSH and a PAL monitor.