Why does my partial reconfiguration design give invalid recommendations?

Due to a problem in the Quartus® II software version 13.0, if you are using partial reconfiguration, you may see the following warning in the Design Partitions Window

Region <region name> contained logic from multiple partitions (<region name>, <region name>). Ensure that each region contains logic from one partition.

Additionally, you may see this warning in the Incremental Compilation Advisor Team-Based Recommendations

Do Not Place Logic From Multiple Partitions in One LogicLock Region

This recommendation is incorrect for for partial reconfiguration designs and should be ignored. If you are not using partial reconfiguration, your design should be changed to avoid this warning.

This problem is scheduled to be fixed in a future release of the Quartus® II software.