Adaptive optics (AO) systems have improved astronomical imaging capabilities significantly over the last decade, and have the potential to revolutionize the kinds of science done with 4-5m class ground-based telescopes. However, provided sufficient detailed study and analysis, existing AO systems can be improved beyond their original specified error budgets. Indeed, modeling AO systems has been a major activity in the past decade: sources of noise in the atmosphere and the wavefront sensing WFS) control loop have received a great deal of attention, and many detailed and sophisticated control-theoretic and numerical models predicting AO performance are already in existence. However, in terms of AO system performance improvements, wavefront reconstruction (WFR) and wavefront calibration techniques have commanded relatively little attention. We elucidate the nature of some of these reconstruction problems, and demonstrate their existence in data from the AEOS AO system. We simulate the AO correction of AEOS in the I-band, and show that the magnitude of the `waffle mode' error in the AEOS reconstructor is considerably larger than expected. We suggest ways of reducing the magnitude of this error, and, in doing so, open up ways of understanding how wavefront reconstruction might handle bad actuators and partially-illuminated WFS subapertures.