Spanner in the works for you here.....
I get this continued tracking also but I use the keyboard to move the Shkval.
I find that this continued tracking orcurs when Im targetting civ traffic that moving along a road say from left to right @ 6Km. What happens is I target it, launch a missile, watch it explode then the Shkval continues to track where it should be before the target copped it.
Now if I try to move the shkval/retarget something else it keeps tracking in the direction the target was moving and it continues to do this until I enter Nav mode (backspace) ans then return to targeting mode (o).