SPI waveform on Raspberry Pi is not clean, and I'm wondering why
The spikes at the rise and fall of the blue signal are probably due to probe inductance (aka long GND wire connection). Try using as short as possible GND connection.
Also as much as possible, for scope measurement get rid of the hookup wires and use the probe as close as possible to the final destination of the signal. For example if the Pi is the SPI master so in order to probe the SCK signal try placing the probe as close as possible to the FPGA SCK input.

Also note that the disturbance on the purple signal is synchronized with the rise and fall of the blue signal. This means it is due to cross talk between the signals. If possible try to increase the distance between the signals.