I am experiencing this problem over multiple months (maybe a year) already. I hoped it will get soon fixed via standard package upgrades, but as it still persist and is really annoying I googled around and now send this message in hope to increase priority a bit ;).
In my case there are several facts I would like to share: 1) Plane desktop, no lid, no auto sleeping in setup. this particular Debian instalation worked without this issue for many years before. Only standard aptitude updates done under manual control, no dist-upgrade/updates. 2) As I do have auto-logging user (myself :) ) in KDE, if I choose reboot it simply relogs back to deskotp. 3) I do use only sleep (now called suspend to ram) via KDE kicker's Leave- >suspend menu. Never experienced problems with waking up. 4) Workaround with sudo reboot -f works allways, however often I am getting some file reparations/removals reported on next boot. As I reboot often on dual-boot system, this scares me a bit. 5) Sometimes (about 1/4 cases) reboot works normally from KDE. uname -a Linux <censored> 4.6.0-1-amd64 #1 SMP Debian 4.6.2-2 (2016-06-25) x86_64 GNU/Linux Pavel Mendl