This is somewhat difficult for me to reproduce but I'll try to see what I can do. 
This is a pretty serious issue, unfortunately =/.

I had the same problem yesterday in naxx. I could not use clique with grid but with the wow frames it worked 
perfectly. I was disconecting a lot then, so it could be the same bug. If Im not wrong I changed my frames to "25 
man w/tank" and then I changed it again. Im not sure if it was bugged before or after I did that. Hope it helps.

Yeah it's REALLY difficult for me to test this, since there are very few places where I can be in combat while 
logging in.  It really will end up having to do with the unit frames and when/how they are registering for click-
casting so I'm not sure there is much I can do to help things.

If anyone has ideas for HOW i can test this, I'm all ears.

Hi again. I can confirm this bugg. As u can see it happened in a run of naxx a few days ago. Yesterday on trash i 
got DC during combat, and when logged in my clique didn't work on grid. On the other frames it worked 
perfectly. I closed wow completly and open it again, logged in and it worked all ok.

DC= Screen freezes and i get back to the log in screen with a message box that says "You have been 
disconnected from the server". So i didn't "Alt +F4" and nothing like that, server kicked me out.

Hope it helps. Sorry for my bad english.

Hi again. I forgot to say something. Maybe you can try to be in battle with a party, and use Alt + F4. Log back in 
and see if the bugg procs. Cya.

I can REPRODUCE the issue, btu that doesn't really help me.  I need to be able to reproduce it repeatedly over a 
longer period of time in order to fix it.  However, the fact that it works with some frames and not others indicates 
to me that it isn't a problem Clique can solve.. its how Clique is being used.  I'll continue to try and troubleshoot 
it.

Seems to be when using Clique with Grid. A really easy way to test this, is just
invite someone to your group when you are in combat, then you will see during that
encounter, you cannot use Grid+Clique to heal that person. When combat ends,
Grid+Clique will work on that person. Almost seems like grid isn't registring their
unit frames during combat or something.

You will still be able to target other unit frames and heal with Clique.

I may have a fix for this in 3.2 with a new function Blizzard has provided, but we will have to see.