the nature of your problem is not clear to me. I can think at least of four cases:
1. The disturbances are caused by coupling to sources of interference. If possible, suppress the disturbances at the sources. If not, maximize the distance between the sources and the signal traces; shield the traces, e.g. by using striplines in PCBs with at least 4 layers; use differential signals.
2. The gating is applied to an analog signal at the input of an ADC, and the disturbances are the inherent fluctuations of the signal. Use a sample-and-hold circuit (most ADCs are already equipped with one).
3. The gating is applied to a digital signal which is generated on the same PCB. Try to synchronize the generation and the gating in such a way that the signal is stable for a setup time before and a hold time after the edge of the gating signal.
4. The gating is applied to an external digital signal which cannot be synchronized. In order to avoid metastable states, route the signal through an edge triggered flipflop which is clocked by the same gating signal. The disadvantage of this approach is that the gated signal is delayed for one cycle of the gating signal.
I recommend using Micro-Cap (http://www.spectrum-soft.com/download/download.shtm). All EE's at Emerson used Micro-cap, even though it cost $4,000 each. There are no other electronic SPICE modeling programs even close to Micro-Cap capability.
Micro-Cap is now free. Andy Thompson, owner of Spectrum Software, has retired.
Micro-Cap does worst case analysis --- changing the tolerances of components --- changing the temperature --- etc. And it is easy to use.
I have used Micro-Cap for all of my electronic designs since 2001. When I tested prototypes, they worked exactly as the model predicted.
The website --- https://NDAcademy.FoxPing.com/ --- 2.8 Electronic Cascade RC Filters --- and --- 7.2 Electronic SPICE Models --- provide examples.