Hopper set up under rail to pull items from minecart crashes the game whenever it takes any items. Putting items directly into the hopper also produces a crash. See screenshot for set-up. Removing the comparator from the set-up allows the game to function normally (though obviously breaks the redstone mechanism). Taking off the rail also seems to allow the game to run normally.

This issue has occurred on Windows version as well, multiplayer and singleplayer. I was able to reproduce it every time I built this set-up.

Tried to duplicate issue on 15w45a, but could not. This set up seems to work in that snapshot, and items are pulled without breaking the game.

Crash report:
---- Minecraft Crash Report ----
// Surprise! Haha. Well, this is awkward.

Time: 11/15/15 9:12 PM
Description: Exception while updating neighbours

java.lang.IllegalArgumentException: Cannot get property arg

{name=shape, clazz=class ajh$b, values=[north_south, east_west, ascending_east, ascending_west, ascending_north, ascending_south]}

as it does not exist in aqu

{block=minecraft:unpowered_comparator, properties=[facing, mode, powered]}

at aqu$a.c(SourceFile:165)
at ane.a(SourceFile:115)
at ane.a(SourceFile:102)
at ane.b(SourceFile:136)
at ajh.a(SourceFile:454)
at ahm.e(SourceFile:447)
at ahm.a(SourceFile:421)
at akj.h(SourceFile:209)
at ant.b(SourceFile:130)
at arv.a(SourceFile:441)
at ahm.a(SourceFile:312)
at akj.b(SourceFile:68)
at lp.a(SourceFile:646)
at lp.d(SourceFile:215)
at net.minecraft.server.MinecraftServer.D(SourceFile:616)
at net.minecraft.server.MinecraftServer.C(SourceFile:552)
at bxw.C(SourceFile:154)
at net.minecraft.server.MinecraftServer.run(SourceFile:456)
at java.lang.Thread.run(Thread.java:745)

A detailed walkthrough of the error, its code path and all known details is as follows:
---------------------------------------------------------------------------------------

– Head –
Stacktrace:
at aqu$a.c(SourceFile:165)
at ane.a(SourceFile:115)
at ane.a(SourceFile:102)
at ane.b(SourceFile:136)
at ajh.a(SourceFile:454)

– Block being updated –
Details:
Source block type: ID #94 (tile.diode // ant)
Block: minecraft:golden_rail[powered=true,shape=east_west]
Block location: World: (-138,65,60), Chunk: (at 6,4,12 in -9,3; contains blocks -144,0,48 to -129,255,63), Region: (-1,0; contains chunks -32,0 to -1,31, blocks -512,0,0 to -1,255,511)
Stacktrace:
at ahm.e(SourceFile:447)
at ahm.a(SourceFile:421)
at akj.h(SourceFile:209)
at ant.b(SourceFile:130)
at arv.a(SourceFile:441)
at ahm.a(SourceFile:312)
at akj.b(SourceFile:68)

– Block being ticked –
Details:
Block: minecraft:powered_repeater[delay=1,facing=east,locked=false]
Block location: World: (-136,65,60), Chunk: (at 8,4,12 in -9,3; contains blocks -144,0,48 to -129,255,63), Region: (-1,0; contains chunks -32,0 to -1,31, blocks -512,0,0 to -1,255,511)
Stacktrace:
at lp.a(SourceFile:646)
at lp.d(SourceFile:215)

– Affected level –
Details:
Level name: Hopper Test
All players: 1 total; [lr['Hirokitkichiro'/119, l='Hopper Test', x=-136.46, y=65.00, z=57.12]]
Chunk stats: ServerChunkCache: 441 Drop: 0
Level seed: 8871630801195048466
Level generator: ID 00 - default, ver 1. Features enabled: true
Level generator options:
Level spawn location: World: (-136,64,48), Chunk: (at 8,4,0 in -9,3; contains blocks -144,0,48 to -129,255,63), Region: (-1,0; contains chunks -32,0 to -1,31, blocks -512,0,0 to -1,255,511)
Level time: 2148 game time, 2148 day time
Level dimension: 0
Level storage version: 0x04ABD - Anvil
Level weather: Rain time: 52387 (now: false), thunder time: 173427 (now: false)
Level game mode: Game mode: creative (ID 1). Hardcore: false. Cheats: true
Stacktrace:
at net.minecraft.server.MinecraftServer.D(SourceFile:616)
at net.minecraft.server.MinecraftServer.C(SourceFile:552)
at bxw.C(SourceFile:154)
at net.minecraft.server.MinecraftServer.run(SourceFile:456)
at java.lang.Thread.run(Thread.java:745)

– System Details –
Details:
Minecraft Version: 15w46a
Operating System: Mac OS X (x86_64) version 10.11.1
Java Version: 1.8.0_60, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 473789992 bytes (451 MB) / 728760320 bytes (695 MB) up to 2863661056 bytes (2731 MB)
JVM Flags: 1 total; -Xmx3G
IntCache: cache: 0, tcache: 0, allocated: 12, tallocated: 94
Profiler Position: N/A (disabled)
Player Count: 1 / 8; [lr['Hirokitkichiro'/119, l='Hopper Test', x=-136.46, y=65.00, z=57.12]]
Type: Integrated Server (map_client.txt)
Is Modded: Probably not. Jar signature remains and both client + server brands are untouched.