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.