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Set up a document with a sub-document in an array:

db.docs.insert({ "data": [{ "name": "Kimberly" }] })

Attempt a JavaScript match as done by the poster:

db.docs.find({ "data": { "$elemMatch":{ "$where" : "this.name.toLowerCase().indexOf('kim') ==0" } } });

Produces the error in 2.6:

error: { "$err" : "Can't canonicalize query: BadValue $elemMatch cannot contain $where expression", "code" : 17287 }

Which clearly seems intentional, but in prior versions the query produces a matching result without throwing the error.
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Set up a document with a sub-document in an array: db.docs.insert({ "data" : [{ "name" : "Kimberly" }] }) Attempt a JavaScript match as done by the poster: db.docs.find({ "data" : { "$elemMatch" :{ "$where" : " this .name.toLowerCase().indexOf( 'kim' ) ==0" } } }); Produces the error in 2.6: error: { "$err" : "Can't canonicalize query: BadValue $elemMatch cannot contain $where expression" , "code" : 17287 } Which clearly seems intentional, but in prior versions the query produces a matching result without throwing the error.

Different behavior of $where within $elemMatch from 2.4 version to 2.6 the issue was raised in this question

It is noted to the poster that they should not be using the type of query as shown as the results can be achieved by other means.

This probably requires a documentation patch to cover the changed behavior.

duplicates

SERVER-12439 $where in $elemMatch no longer valid in 2.5.5-pre

SERVER-13503 The $where operator should not be allowed under $elemMatch

is related to

DOCS-3449 Doc that $where must be top-level