Minecraft Version: 1.9
Operating System: Linux (amd64) version 3.19.0-33-generic
Java Version: 1.8.0_72, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 381534640 bytes (363 MB) / 1162870784 bytes (1109 MB) up to 1431830528 bytes (1365 MB)
JVM Flags: 2 total; -Xms1024M -Xmx1536M
IntCache: cache: 0, tcache: 0, allocated: 12, tallocated: 94
CraftBukkit Information:
Running: CraftBukkit version git-Bukkit-32587ed (MC: 1.9) (Implementing API version 1.9-R0.1-SNAPSHOT) true
Plugins:

Received this crash from killing any mob with bow.
Tested multipule times on: Zombie, Skeleton, Spider, Cow, Creeper.

EDIT: There is a scoreboard objective for 'totalKillCount'
EDIT2: Killing things with a sword has no change. Objectives like stat.crouchOneCm do not cause crashes.

I just had a slightly different version of this error and then crash the server.

I had scoreboard objective totalKillCount Guardian displayed on the sideboard
I only added the scoreboard about 2 minutes before I updated the server to 1.9

after the error I had one player with a score of 0 on the board.

19:57:44 FATAL]: Error executing task
java.util.concurrent.ExecutionException: java.lang.ClassCastException: net.minecraft.server.v1_9_R1.ScoreboardScore cannot be cast to net.minecraft.server.v1_9_R1.ScoreboardObjective
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:1.8.0_40]
at java.util.concurrent.FutureTask.get(FutureTask.java:192) ~[?:1.8.0_40]
at net.minecraft.server.v1_9_R1.SystemUtils.a(SourceFile:46) [spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at net.minecraft.server.v1_9_R1.MinecraftServer.D(MinecraftServer.java:721) [spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at net.minecraft.server.v1_9_R1.DedicatedServer.D(DedicatedServer.java:400) [spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at net.minecraft.server.v1_9_R1.MinecraftServer.C(MinecraftServer.java:660) [spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at net.minecraft.server.v1_9_R1.MinecraftServer.run(MinecraftServer.java:559) [spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_40]
Caused by: java.lang.ClassCastException: net.minecraft.server.v1_9_R1.ScoreboardScore cannot be cast to net.minecraft.server.v1_9_R1.ScoreboardObjective
at net.minecraft.server.v1_9_R1.EntityHuman.b(EntityHuman.java:462) ~[spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]
at net.minecraft.server.v1_9_R1.EntityLiving.die(EntityLiving.java:952) ~[spigot-vanilla.jar:git-Spigot-1a196e1-92602ad]

Full error...
http://paste.md-5.net/vutedumuxu.avrasm

About a minute later the whole server crashed with this:
http://paste.md-5.net/jativofimi.avrasm

I have disabled the scoreboard for now.
This server only has 5 plugins , PermissionsEx, WorldEdit, WorldBorder, WorldGuard and CommandBook

[20:13:57 INFO]: This server is running CraftBukkit version git-Spigot-1a196e1-92602ad (MC: 1.9) (Implementing API version 1.9-R0.1-SNAPSHOT)
[20:13:57 INFO]: Checking version, please wait...
[20:13:57 INFO]: You are running the latest version

Might be related to this?

https://hub.spigotmc.org/jira/browse/SPIGOT-1561

There was only one player on the map. He says he was using Elytra and the server crash happened when he landed. Cannot reproduce.

I've now added some parts of the server log (see new attachment) when the crash happened as well. "ABC123DEF" is the user (I've masked user names and IP). "Player2" is not relevant.

From the server log it might seems to have something to do with damage. Might be something related to damage when landing with Elytra?

{{Caused by: java.lang.AssertionError: Unhandled damage of EntityPlayer['ABC123DEF'/1431, l='world', x=-42.14, y=72.69, z=-347.30](ABC123DEF at -42.139239109$
at org.bukkit.craftbukkit.v1_9_R1.event.CraftEventFactory.handleEntityDamageEvent(CraftEventFactory.java:529) ~[craftbukkit-1.9.jar:git-Bukki$
}}

>scoreboard objectives list
[21:02:50 INFO]: Showing 6 objective(s) on scoreboard:
[21:02:50 INFO]: - Score: displays as '10' and is type 'dummy'
[21:02:50 INFO]: - money: displays as 'money' and is type 'dummy'
[21:02:50 INFO]: - Kills: displays as 'Kills' and is type 'totalKillCount'
[21:02:50 INFO]: - 100000: displays as '100000' and is type 'dummy'
[21:02:50 INFO]: - health: displays as 'health' and is type 'health'
[21:02:50 INFO]: - ABC123DEF: displays as '11' and is type 'dummy'

Any steps to reproduce? What is your scoreboard configuration?