Negation predicates like $ne or $not did not make use of an index if the index was a "multikey" index (where the indexed fields contained arrays).
Queries with negation predicates were scanning the entire collection, which is inefficient and can cause disruption in the working set.
In some cases, the query can be rewritten (for example with $gt and $lt predicates) to eliminate the negation predicate.
Multikey index usage has been enabled for negation predicates.
All recent production releases up to and including 2.6.0 are affected.
The patch is included in the 2.6.1 production release.