CRJ-900 First Officer reported troubleshooting a malfunctioning autopilot while on an RNAV approach resulted in low altitude alert from ATC and a CFTT event.

Narrative

On Day 0 while operating Aircraft X ZZZ1 to ZZZ I received a low altitude alert from ZZZ Tower. We will doing the RNAV to [Runway] XX. We were fully configured before ZZZZZ per our company standards. The autopilot was on with VNAV on following the snowflake. In between ZZZZZ and ZZZZZ1 the autopilot started performing poorly so I immediately disconnected the autopilot. Shortly after this the Captain pointed out I was getting a little low while attempting to fix the issue; ATC give us a low altitude alert. We immediately fixed the altitude issue and continued the approach without issue. I called our Company to attempt to get more data on the flight to learn more about the situation and insure it doesn't happen again but I have yet to receive said data.Cause: I believe I should have disconnected the autopilot earlier; usually I disconnect it once fully configured to trim the airplane to a comfortable flying position and to maintain a consistent descent. Since I disconnected so quickly I think it cause me to go low on the approach.