Myriad of (relatively minor) issues on my rMBP in the last few days
We've had a couple of machines at work in a similar state, they were brought back to normal operation by starting in safe boot then moving the Containers folder from the user's Library folder to the desktop. This has the effect of clearing the startup caches, performing a disk check and resetting sandboxed applications back their default settings.

A new Containers folder will be automatically created. Any applications that have lost important data after moving the Containers folder can be restored by copying the relevant folder from the old Containers folder to the new one - I always make a copy of the ARD folder as any custom UNIX commands will be lost otherwise.

As a matter of course I would also want to run a disk permissions check and give the drive structure a check with DiskWarrior.