Adding MultiKey index breaks IXSCAN

Hi, I have this legacy schema

{
    "root" : [ 
        {
            "key" : [ 
                [ 
                    "value", 
                    ...
                ], ...
            ]
        }, ...
    ]
}

I’m querying the documents with

"root":{
   "$elemMatch":{
      "key.0":{ // can be 0, 1, 2, etc.
         "$elemMatch":{
            "$eq":"value" // only value that can change
         }
      }
   }
}

That’s currently working but it’s really slow, I’ve tried adding a multi key index {"root.key.0": 1}, totalIndexSize() reports about 59kb more that without it, that means is does have something but when I run the exact same query I no longer get any results.
Explain outputs the following:

"inputStage" : {
    "stage" : "IXSCAN",
    "nReturned" : 0,
    "executionTimeMillisEstimate" : 0,
    "works" : 1,
    "advanced" : 0,
    "needTime" : 0,
    "needYield" : 0,
    "saveState" : 0,
    "restoreState" : 0,
    "isEOF" : 1,
    "invalidates" : 0,
    "keyPattern" : {
        "root.key.0" : 1
    },
    "indexName" : "indexTest",
    "isMultiKey" : true,
    "multiKeyPaths" : {
        "root.key.0" : [ 
            "root", 
            "root.key"
        ]
    },
    "isUnique" : false,
    "isSparse" : false,
    "isPartial" : false,
    "indexVersion" : 2,
    "direction" : "forward",
    "indexBounds" : {
        "root.key.0" : [ 
            "[\"value\", \"value\"]"
        ]
    },
    "keysExamined" : 0,
    "seeks" : 1,
    "dupsTested" : 0,
    "dupsDropped" : 0,
    "seenInvalidated" : 0
}

It’s clearly trying to match and the “indexBounds” is ok but it says “keysExamined”: 0.
I’ve tried several index combinations like “root.key”, “root.0.key.0”, “root.0.key.0.0” but those have indexBounds: [MinKey, MaxKey] so they’re not useful.
If I use $regex instead of $eq I get “keysExamined”: 1 but still no results.
I’ve also tried to see if there was any way of seeing what was really in the index but I don’t know how to do that.
We do have a new schema but this one can’t be migrated without manually checking each document, so it’s not really a choice.
Is there any way to check the index or indexing so that this query works faster?