New South Wales
You are probably misinterpreting what happens when you ward two or more doom at once. That is a property of the ward action and does not apply when you aren't using a ward action. The rule is:
AH3 RR wrote:
494.3 If you remove two or more doom as part of a ward
action, you gain one remnant.
Resolving an anomaly encounter is not a ward action, but it just happens to still grant you a remnant in most (possibly all) cases where you remove two or more doom. There is no 'additional' remnant to gain as it is not due to a ward action.
Similarly, if you kill a monster that has the remnant icon without taking an attack action (e.g., using Michal McGlen's Ol' Boiler), you do not get a remnant for killing it. Remnants from the icon are only given when a monster is defeated during an attack action.