Do character abilities still trigger if the requirements are met through cards played but negated by the opponent or otherwise?
For example, Wave 1
Thundercracker’s bot mode ability --> Player 1 uses
Supercharge, but player 2 reveals
Infiltrate and negates Supercharge. Does Thundercracker's ability still trigger because an action was played? Meaning he would indeed get +1?
[Source: WotC] 
The
Infiltrate will scrap the action you played and negate its effect, but
Thundercracker’s ability still triggers because you played an action.
This is also true for other cards that cancel an Action, such as
Jam Signals, Overrule, and
Speed Trap, and for any other effects (like Thundercracker) related to playing a card.
I am playing Nightbird in alt mode. My opponent plays
Brainstorm and 2 follow-up actions. I reveal a Secret Action to stop 1 of the follow-ups. Does my opponent still take 3 damage?
[Source: Aequitas]
Yes. Even when cancelled by an action such as
Infiltrate,
Jam Signals, or Overrule, a card is still played and an effects that refer to cards, or number of cards, being played still occur. Another example would be Thundercracker, Mach Warrior's bot mode effect.
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