Playing with 3.2.0-rc4 I have found that the db.stats() command is always informing the size of indexes as 4096 bytes.
MongoDB Enterprise inMem:PRIMARY> db.stats()
{
"db" : "POCDB",
"collections" : 1,
"objects" : 1876714,
"avgObjSize" : 285.37579247557164,
"dataSize" : 535568745,
"storageSize" : 535568745,
"numExtents" : 0,
"indexes" : 1,
"indexSize" : 4096,
"ok" : 1
}
This is also affecting compass index size report.