We have a 2.4 system thats recently been upgraded to 2.6 and then 3. Everything appeared to be working, until we saw this message:

Found $db field without a $id before it, which is invalid.

A quick google found this code:

https://github.com/mongodb/mongo/blob/master/src/mongo/db/exec/update.cpp#L98

and a quick look in our DB reveals the order is incorrect (see attachment). This isn't something we've done (we use Doctrine). However how can we easily fix this problem? We potentially have 1000s of DBRefs in the wrong order.

Thanks for your help,
Ben