While running the latest build of Spigot or CraktBukkit, if you run into a wall while flying with Elytra, you will be kicked. The console then spits out:
?? [00:13:59 WARN]: Failed to handle packet for /127.0.0.1:61091
net.minecraft.server.v1_9_R1.ReportedException: Ticking player
at net.minecraft.server.v1_9_R1.EntityPlayer.k_(EntityPlayer.java:320) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.PlayerConnection.c(PlayerConnection.java:136) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.NetworkManager.a(NetworkManager.java:223) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.ServerConnection.c(SourceFile:187) [craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.MinecraftServer.D(MinecraftServer.java:746) [craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.DedicatedServer.D(DedicatedServer.java:361) [craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.MinecraftServer.C(MinecraftServer.java:630) [craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.MinecraftServer.run(MinecraftServer.java:534) [craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_73]
Caused by: java.lang.AssertionError: Unhandled damage of EntityPlayer['S1rSm0k3s4l0t'/107, l='world', x=-103.30, y=78.19, z=-7.70](S1rSm0k3s4l0t at -103.30000001192093,78.19114424738139,-7.699999988079071) from flyIntoWall
at org.bukkit.craftbukkit.v1_9_R1.event.CraftEventFactory.handleEntityDamageEvent(CraftEventFactory.java:529) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at org.bukkit.craftbukkit.v1_9_R1.event.CraftEventFactory.handleLivingEntityDamageEvent(CraftEventFactory.java:572) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityLiving.damageEntity0(EntityLiving.java:1196) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityHuman.damageEntity0(EntityHuman.java:834) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityLiving.damageEntity(EntityLiving.java:804) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityHuman.damageEntity(EntityHuman.java:758) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityPlayer.damageEntity(EntityPlayer.java:498) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityLiving.g(EntityLiving.java:1574) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityHuman.g(EntityHuman.java:1429) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityLiving.n(EntityLiving.java:1913) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityHuman.n(EntityHuman.java:338) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityLiving.m(EntityLiving.java:1747) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityHuman.m(EntityHuman.java:141) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
at net.minecraft.server.v1_9_R1.EntityPlayer.k_(EntityPlayer.java:239) ~[craftbukkit-1.9.jar:git-Bukkit-ea28c1e]
... 8 more
[00:13:59 INFO]: S1rSm0k3s4l0t lost connection: Internal server error
[00:13:59 INFO]: S1rSm0k3s4l0t left the game.??

I've tried this with and without plugins, and can confirm it does not occur in the Vanilla Minecraft Server under the exact same conditions.