I can confirm this is an issue. The console output is the same except it doesn't exit.
SIGTERM is ignored so I have to SIGKILL.
Tested on:
CentOS 6.5
openjdk version "1.8.0-internal"
OpenJDK Runtime Environment (build 1.8.0-internal-0)
OpenJDK 64-Bit Server VM (build 25.0-b57-internal, mixed mode)
I just did a few tests and it only happens if people are still connected when you do /stop. Entering the command into an empty server (i.e. 0 players online) will successfully exit.
Also confirmed on:
Kubuntu 14.04
java version "1.8.0_11"
Java(TM) SE Runtime Environment (build 1.8.0_11-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.11-b03, mixed mode)