Andy,
These might be from steps in input / output impedance at those frequencies. You can remedy this by adding a 3 dB pad to the output of the TG and input of SA before “store thru” and keep them on for all measurements. This improves return loss by 6 dB and cleans up impedance mismatch-related measurement error.
Another thing you can do is “store thru” with a similar length cable to the circuit you will be testing.
If these steps occur with 30-50 dB insertion loss, you may need to “store 20 dB pad” to get rid of them.