This... is a change in MongoDB 2.6.0, no longer accepting bson object in the $in clause.
This particular issue is being tracker
as a PHP driver bug at https://jira.mongodb.org/browse/PHP-1051
The MongoDB PHP Driver will an PHP Array into BSON Array (accepted by the $in operator) when the PHP array is: Sequential numerically indexed, starting from 0
Which does not start with index 0. The MongoDB PHP driver therefore converts this into a BSON Object... Leading to validation error in MongoDB as it expected an array.
Now, since the MongoDB PHP driver does not do parse your MongoDB query we cannot know which array should be exempted from this serialization rule.
The workaround is, as mentioned above, is to ensure your PHP arrays are numerically indexed, starting from 0. The easiest way to do that is to run