A case has been seen where the clock placer oversubscribed a vertical branch of the clock routing resources which have a limit of supporting up to 12 different clock domains using either BUFR or BUFG clock buffers. The clock region involved contained 11 global clock domains and 4 regional clock domains. The clock placer should have ensured that no more than 12 were placed in any one branch.
This issue has been fixed in the clock placer for the 2012.3 tools which is scheduled for release in mid-October.
Meanwhile, you can avoid this problem with floorplanning techniques to prevent the placement conflict, either by moving clock domains out of the clock region or by partitioning the clock region to separate the conflicting clock domains.