The steps:

Step 1.
Add an object {_id : 1, a : [1, 2]} to the empty collection test:

> db.test.drop()
> db.test.insert({_id : 1, a : [1, 2]})

Step 2.
Let's try to pop from a[-2], i.e. from non existent data. This is nonsense perhaps but it changed behaviour.

> db.test.update({_id : 1}, {$pop : {"a.-2" : 1}})
WriteResult({
        "nMatched" : 0,
        "nUpserted" : 0,
        "nModified" : 0,
        "writeError" : {
                "code" : 16837,
                "errmsg" : "cannot use the part (a of a.-2) to traverse the element ({a: [ 1.0, 2.0 ]})"
        }
})

The above pop fails and data are not changed. In v2.4.9 this nonsense pop was silently ignored (if I am not mistaken).

Step 3.
Now let's pop from a[3], i.e. also from non existent data.

> db.test.update({_id : 1}, {$pop : {"a.3" : 1}})
WriteResult({ "nMatched" : 1, "nUpserted" : 0, "nModified" : 1 })

> db.test.find()
{ "_id" : 1, "a" : [ 1 ] }

The result is presumably incorrect. {$pop : {"a.3" : 1}} instead of failing (like with a.-2 in v2.6) or doing nothing (like with the same case in v2.4.9) it removes data from 'a' itself, i.e. actually performs another operation: {$pop : {"a" : 1}}.