I ran across the case where the bounding box query would sometimes give me a "point not in range" error with no discernible reason that I can find. You can recreate the issue with the following:

db.foo.insert({ point :

{ x : -15000000, y : 10000000 }

})
db.foo.ensureIndex(

{ point : "2d" }

,

{ min : -21000000 , max : 21000000 }

)
db.foo.find({point: {"$within":

{"$box": [[-20000000, 7000000], [0, 15000000]]}

} })

The console shows:
error:

{ "$err" : "point not in range" }

The mongod log shows:
Sun Apr 11 00:50:35 User Exception 13027:point not in range
Sun Apr 11 00:50:35 Assertion: 10362:point not in range
0x505bb4 0x56219c 0x5fa2da 0x5feb2f 0x6a9a72 0x6bbde0 0x7f372ecb03ba 0x7f372e272fcd
bin/mongod(_ZN5mongo11msgassertedEiPKc+0x204) [0x505bb4]
bin/mongod(_ZN5mongo8runQueryERNS_7MessageERNS_12QueryMessageERNS_5CurOpE+0x182c) [0x56219c]
bin/mongod [0x5fa2da]
bin/mongod(_ZN5mongo16assembleResponseERNS_7MessageERNS_10DbResponseERK11sockaddr_in+0x118f) [0x5feb2f]
bin/mongod(_ZN5mongo10connThreadEv+0x242) [0x6a9a72]
bin/mongod(thread_proxy+0x80) [0x6bbde0]
/lib/libpthread.so.0 [0x7f372ecb03ba]
/lib/libc.so.6(clone+0x6d) [0x7f372e272fcd]
Sun Apr 11 00:50:35 Caught Assertion in runQuery ns:test.foo massert:point not in range
Sun Apr 11 00:50:35 ntoskip:0 ntoreturn:0
Sun Apr 11 00:50:35 query:{ point: { $within: { $box: { 0:

{ 0: -20000000.0, 1: 7000000.0 }

, 1:

{ 0: 0.0, 1: 15000000.0 }

} } } }
Sun Apr 11 00:50:35 query test.foo ntoreturn:0 exception 1ms

However running the query with a different bounding box like so:
db.foo.find({point: {"$within":

{"$box": [[-20000000, 0], [0, 15000000]]}

} })
WIll find the point as expected.

I've run into quite a few of these that act the same way with various bounding boxes and data, any help will be greatly appreciated!