In this paper, we describe two issues that have been discovered during the design of a flight control system of Mars airplane and an experimental vehicle. The first issue is that both, the experimental and Mars aircraft, easily tend to entry to the backside region. This has been observed even at higher speeds and lower angle of attack than in conventional aircraft due to different flight environments and aerodynamic characteristics. The second issue arises due to the aircraft being lightweight and able to fly at high cruising speeds. This results in a high natural frequency of short period mode. Due to this high natural frequency, usually negligible time delay effects have a significant effect. Therefore, the phase margin of the system decreases and its control performance tends to deteriorate.