Bug with recreation modules. I created a jump gate defence base (military) with recreational facilities and a 3-month deployment time, and deployed it alone on a jump point. A few months later, I received a message that it's morale was dropping due to lack of shore leave. I designed a bare-bones civilian "ship" that only contains recreational facilities and used Fast OB to add it to the task group with my JG defence base. After running an increment, the defence base is now reporting that it has had shore leave.
I used SM mode to unlock my defence base design to remove the recreational facilities, since it clearly isn't working in my military base, and updated my deployed base by viewing it in the Ships screen. Some time later, I happened to look at the JG defence task group and noticed morale was at 23%! I had received no notifications. I also had a separate task group stationed at the same location whose Crew Months counter was increasing. Again through SM mode, I updated the defence base to include the recreational facilities, updated in Ships screen, incremented, and now both the defence base and my fleet are happy.
It seems that, in order to gain the benefit of the recreational facilities, at least two ships in one TG need to have one of these monstrous facilities installed. I haven't tested further than this.
EDIT: I ran into additional problems with my third JG defence base deployed, assumed it had something to do with using Fast OB to add my recreation facility "ship" to the task group. I used a tug to haul the rec facility a few hours away from the JG task group, then hauled it back and added it to the JG task group. Everyone is happy. For my fourth base, i also built the rec facility "ship", and hauled both out to a jump point. Unfortunately, I can't find the secret ceremony to make it work for this group. I've hauled the rec facility ship a few hours away and hauled it back, I've sent a fleet task group away and back to the jump point, I've hauled the rec facility all the way back to a planet and kept it there for a month before hauling it back and adding it to the JG task group, and I've tried keeping the rec facility ship in my tug task group at the same location as my JG task group and fleet task group. Nothing seems to make the crew happy and morale continues to drop.
EDIT 2: Meanwhile, the fifth defence base deployed happily provides it's rec facilitiy benefit to itself without any other facilities or ships present, including the rec facility "ship" I had to make the first time I deployed a JG defence base on its own. I'm having trouble finding a repeatable series of steps that will help in isolating this error.
EDIT 3: Tug group grabbed the fourth defence base and it's rec facility companion "ship" and started hauling them back to Earth. 30 days into the trip, still at least 250 Mkm from Earth and with either 7 or 11 months on the crew months counter, the defence base crew have somehow now had their shore leave, and their crew counter is at 0, while the companion ship, whose clock was somewhat higher than the defence base's clock, has had it's clock reduced to 2.07 months. Hopefully this seemingly-random series of events makes sense to you and points you to the offending piece of code.