On hydrophobic surfaces, roughness may lead to a transition to a superhydrophobic state, where gas bubbles at the surface can have a strong impact on a detected slip. We present two-phase lattice Boltzmann simulations of a Couette flow over structured surfaces with attached gas bubbles. Even though the bubbles add slippery surfaces to the channel, they can cause negative slip to appear due to the increased roughness. The simulation method used allows the bubbles to deform due to viscous stresses. We find a decrease of the detected slip with increasing shear rate which is in contrast to some recent experimental results implicating that bubble deformation cannot account for these experiments. Possible applications of bubble surfaces in microfluidic devices are discussed.