Not certain on how to recreate, but will try to supply some details:
Ad 1) As Emilia happened only once when paying no attention, not much info nor log saved unfortunately. Thought about damage and/or armour, or some healing happening. I think she was incapacitated by Mafia specialist (maybe rifle) on workshop facility attack. Here is the screen - Elena trying to target her tile:
Ad 2) I had this twice happened with Ray unable to target a tile when he was HtH. Maybe there was a mouseover on an enemy standing next to the tile where now incapacitated unit was or this tile will be in the path. The first time, once I clicked at the enemy -> no targeting anymore. The second time, I just right-clicked to move (see persistent ally thread for the screen).
As for what happened to now incapacitated unit. I don't know yet. Having some logs saved so can do digging as well as play some missions to see on recreation (seeing persistent standing ally is safely in your hands). However, I'm jumping from own work to here and back, not effective at either.
Some [misleading] clues for 2:
-- there were survivalists at play so firearms damage probable
-- There is also an issue when using end turn key at some unsuspected moment (like right after Ray attacked an enemy with bat), it doesn't allow me to end turn, but targeting tiles isn't possible for a moment. Feeling is similar, however, I think this doesn't require changing weapons to refresh itself.
--
there is also suspicion that KOed unit (1st survivalist and then it was Sam) was supposed to act right before Ray's turn. Nope. That was stupid. With Sam it's other way around.
Note: unacessible tile from (1) applies for everybody, whereas (2) is only happening to one ally till he changes weapons.