Wrong SPI Signals in Logic Analyzer
Look closely at the clock decoding, it triggers on both edges so it goes out of sync. The waveform itself looks okay at this zoom level. It may be a bug in the software. Or there is actually a glitch in the waveform so the logic analyzer really sees an extra transition there, do zoom in and take a look. Do note that for about 1 MHz SPI clock, your 500 MHz sampling rate is quite unrealistic.