Dear Pablo, 
I tried to play with your structure and I succeeded. 
First,  run 
x supercell 
always one cell in x- y- and z- directions 
zero shift in all directions 
 Enter your  target lattice type:
P 
(you must choose primitive lattice in order to break 
the symmetries you do not want there). 
Zero vacuum in all directions. 
Then 
cp TiO2-sup_super.struct TiO2-sup.struct 
Edit the TiO2-sup.struct file and find the two Cu atoms. 
Rewrite the space after first Cu to 1. 
Rewrite the space after second Cu to 2. 
Or do these two things comfortably using w2web. 
You must have them inequivalent. 
By the way, are you sure that the vacuum you have for your slab is 
sufficient? When I use slabs I try to have vacuum around 20 bohrs. 
Then  run 
x sgroup 
By checking TiO2-sup.outputsgroup you see that sgroup has chosen 
monoclinic lattice but with all three angles equal to 90 degrees. 
(Space group 56  6 Pm) 
Then, I STRONGLY RECOMMEND TO ERASE ONE OF THE Cu ATOMS, 
probably the one at the position 0 0 0. 
It worked on my computer. 
HTH 
Tomas 

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