$W net$ in the first equation is not the same as $Wnet$ in the second equation.
The first equation relates to $W=Fxd=\Delta KE$ where the work is done displacing the center of mass of the system. It relates to the external energy of the system with respect to an external frame of reference.
$Wnet$ in the second equation is the sum of the first equation plus the work done on the system to change it internal energy (missing is the possibility of Q). The most common type of the latter work is boundary work (expanding or contracting the boundaries of the system).
The complete form of the first law is
Q – W = ΔE = ΔU + ΔKE + ΔPE
ΔE = Total energy change of the system, which is the sum of change in internal and external energy of the system.
ΔKE = Change in kinetic energy of the system as a whole. This relates to a change in the velocity of the center of mass. By the work energy principle:
F x d = ΔKE
ΔPE = Change in potential energy of the system as a whole, such as a change in elevation of the center of mass (change in gravitational potential energy).
Q and ΔU are as always.
W now includes both boundary work and work done on or by the system a whole.