This may or may not be a bug, but I thought I might as well make sure.
While it was raining/storming in the docks, it was not doing the same in 1) Colony- Inner City Ruin and 2) Island - Coastline - Reef.
Also, it's not possible to rest in Island - Coastline - Reef.
Since we're on this subject, it might also be a good idea to make sure the sending system is installed for those areas. I know for sure the skyboxes haven't been activated.