Probe max voltage (50:1)
I suspect you are using ( but you forgot to mention) this probe

Allowable differential voltage
(between + and – terminals)
±140 V (DC + ACpeak) at 50:1 attenuation  (DO NOT USE)
±1400 V (DC + ACpeak) at 500:1 attenuation  ( OK to use)


If your CMRR noise is high then when you put both probes on same line, it will not be a flat line. Use this as your calibration to prevent saturation or to calibrate each probe.

ACtive FET diff probes are also very ESD sensitive so be careful.

There are other tricks such as using twisted pairs to source, keeping leads short, adding Ferrite CM chokes but these will affect transient response so test on a high BW DSO for best results calibrated with a flat line on same square wave.