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The rover's Mars mission was almost a failure on 21st January 2004 due to software, a DOS-based filesystem and not enough flash memory - here's what happened...

Spirit rover - Mars day (Sol) 18...
Extract from the report...

Sol 18 Plan

—The plan for Sol 18 was for the rover to wake up for an early morning UHF communication window with the Odyssey orbiter to downlink yestersol’s data. It would then return to sleep until 8:30 LST, when it would wake up again to warm up the actuators on the High Gain Antenna (HGA) for a DTE X-band communication window. During the DTE window, a sequence would execute to characterize the actuator that controls a mirror in the Miniature Thermal Emission Spectrometer (MTES). The purpose of this activity was to gather calibration data for operating the mechanism at the cold morning temperatures. The rest of the sol would be spent brushing a rock with the Rock Abrasion Tool (RAT). Afternoon DTE and UHF windows were scheduled to downlink engineering and science data.

Sol 18 Observations (what actually happened)...

—The early morning UHF window telemetry showed no problems and the 9:00 LST DTE window started right on time, initially indicating that the vehicle was healthy. The operations team began the uplink of the sequences. Eleven minutes into the window, telemetry showed that uplink errors were detected onboard. The downlink became spotty. At approximately 9:16 LST, the signal dropped out completely, 14 minutes earlier than scheduled. 
At this point, without any more information, poor weather at the ground station (Canberra, Australia) was blamed for the signal dropout.

The operations team expected a beep5 at either 10:00 LST to indicate the new master sequence was onboard and running, or at 10:10 LST to tell us the old sequence was still running. 

The team did not detect the carrier signal for either beep. 

Again, the team blamed the weather at Canberra for the lack of any signal. 

At 11:20 LST, the team commanded a 30-minute high priority HGA communication window, but no signal was received. Again, the Deep Space Network station was the prime suspect, but the team began to suspect antenna pointing problems or telecom hardware failures. 

At 12:45 LST, a beep was commanded and this one was received as predicted, both in start time and duration. This told us that the vehicle was commandable and that none of the onboard system level fault protection responses, that change the uplink rate, had executed. The operations team then commanded the afternoon master sequence to start and they received the beep embedded in the sequence per predict. 

The team breathed a sigh of relief, but it was short-lived. 

Just a half hour later, the team waited for the pre-scheduled 14:00 LST HGA DTE communication window, but no carrier signal was detected.

Read here what happened next.

This was one occasion when software errors were able to be fixed, but there have been other occasions where software errors such as  number conversion, a misplaced symbol or using the wrong units have caused a disaster and cost tax-payers millions of $ - read about them here - 9 famous (and costly) software glitches.