Citation V/Ultra/Encore (C560)
Flight Crew Air Transport Pilot (ATP)
Situational Awareness
Aircraft Equipment Problem Less Severe; Deviation - Altitude Overshoot; Deviation / Discrepancy - Procedural Clearance
Flight Crew Became Reoriented; Flight Crew Returned To Clearance; Flight Crew Overcame Equipment Problem
Human Factors; Aircraft
We were given a crossing restriction at BITLR of 6;000 ft MSL. We started out of FL200 roughly 50-60 nm out from BITLR. Prior to BITLR we requested direct to RULDE off the GPS Rwy 32 in STP. The controller came back and stated that he would clear us instead to BABCO off the ILS Rwy 32 in 10 miles. At 1000 ft prior to level off (6;000 ft). The altitude alert did chime and the light indicator came on and we also verified that the autopilot was armed to capture at 6;000 ft. During this time we got cleared to BABCO intersection for the visual Rwy. 32 into STP. The PM was then entering in the waypoint into the FMS and the PF was both flying and watching the PM entering the information into the FMS. So; around 800 ft below the altitude assigned; the PF reacted by disengaging the autopilot; applying power and pitch up to climb back 6000 ft Upon reaching 6000 ft; the autopilot was reengaged and no further issues. At no time did MSP approach say anything about our altitude. The crew did note that the altitude alert system did NOT alert them to being 200 ft low during this event.During the next flight; the crew noticed several times that the altitude select on the #2 autopilot was disarming and at no time were there any altitude deviations. Each time that there was a new altitude; the altitude alert functioned properly. Approximately 200 ft prior to level off; the attitude select would DISARM. The crew determined that the #2 autopilot is malfunctioning at which point #1 autopilot was used for the remainder of that flight. Once on the ground; the crew notified maintenance.
[Report narrative contained no additional information.]
CE-560 flight crew reported overshooting an altitude restriction when the #2 autopilot malfunctioned.