If during a match you go to tactics screen and replace a player, and then replace that new player straight away, while still on the screen, it counts as a double substitution even though one of them never came on. E.g., I go to my tactics screen and drag Henderson on to Gerrard and then Adam on to Henderson, what should happen is Gerrard off Adam on (as it would in FM), but it takes it instead as Henderson is put on then immediately subbed off, using up one of my 3 subs and not allowing Henderson to be brought on.
While experimenting with this a bit, we found another issue - but on further inspection don't believe it's the same issue that you have. When you try to drag a player over the top of a player it shouldn't do anything. What method are you using to substitute your players? Dragging pitch icons over the substitutes in the grid? Dragging the substitute tile from the grid onto the pitch?
Or solely using the grid to swap the players?
In all cases it should be doing nothing at the moment, although it has been requested that we make it behave as you described in FM.
EDIT: A quick update, it seems to be perfectly normal when you try and perform this action the first time. However, it seems that if you have made a substitution previously, then for some reason this behaviour does occur. if you can confirm/deny that that'd be smashing.