The bunk bed, when one of the sides is obstructed by other furniture or by walls, two characters using the same bed will use the same level of it. I mean, both characters will use the upper bed at the same time. I'd suggest making it so they use both parts of the bunk bed regardless of wich side they aproach it.
Maybe this should go into bug report, but I wasn't sure...

Can Anyone Make a Patch for Mega Cities Towns Merge Mod? Some locations have objects clipping on each other with this mod, but in others, both mods combined makes the interior look real nice.