Having multiple circuits sharing a junction box is very common and permissible as long as they're originating from the same source.
It's a very good idea to keep circuits labeled and bundled but it's not required to idiot proof neutrals from being screwed up by a hack down the line.
New requirement in 2014 - 200.4(B):
Where more than one neutral conductor associated with different circuits is in an enclosure, grounded circuit conductors of each circuit shall be identified or grouped to correspond with the ungrounded circuit conductor(s) by wire markers, cable ties, or similar means in at least one location within the enclosure.
If you have multiple neutrals in an enclosure you now need to somehow identify which neutral goes with which ungrounded conductor(s).
A situation of having a raceway for home runs and splicing onto conductors in cables or even raceways containing only one circuit does provide enough distinction to know which neutral goes with which ungrounded conductor(s) and requires no further identification.
I know this maybe borders on the NEC becoming a design manual, but is a rule that does make more sense then some of those questionable design manual rules, and in most instances does not create much extra work for the installer, but definitely does help the guy that comes along later to figure out what he has to work with.