Reflection on SPI Clock Signal, termination or stub issue?
I had similar issues in one of my designs, but that issue was related to driving 5V-tolerant input (as it was declared by the datasheet - device itself is 3V3) with 5V TTL signal.

I tried a number of termination circuits, starting from series termination as you have it now on the circuit, ending with series resistor and capacitor. With network of resistor and capacitor I was able to smooth the spike, but it affected edges badly.

During the course of my investigation, I got to know that series termination resistor should be as close to source as possible. In your case it is close to destination. This is the first thing I would change.

Next, "5V tolerance" in the mux's datasheet strains me. Such tolerance, to my understanding, while is great in terms on extending application of the device, goes at the expense of additional internal components which would make device "tolerant" (e.g. diodes, resistors). These components may cause some bad effect (however I can only tell you basing on my case), including kind of changes in impedance and thus signal distortions and spikes.

My second advice, if first will not help up to your requirements,  is if you can find native 3V3 I/O mux and use it instead.