My answer is the same as Arnab’s.
How is your initial simulation box defined? For Planar Couette flow (deform xy, as in your input), you need to tell LAMMPS to use a general box, i.e., triclinic. You could add the following line in the file from which you read_data.
0 0 0 xy xz yz
xlo_value xhi_value xlo xhi
ylo_value yhi_value ylo yhi
zlo_value zhi_value zlo zhi
followed by Atoms section etc…
The first line above is the key. See if the log file prints that the box has been built to be triclinic (even though at time t=0, the off diagonal components of the cell matrix are zero)