If you find out your damage deck is missing a card, how do you replace it? Outside of buying a 2nd core set, is this something FFG would replace?

You could contact them and see what your options are. Odds are they'll send you what you're missing.

But there are a number of things I wish FFG would offer for sale, like pegs, bases, damage cards, even dials.

yeah,
Is it missing when you opened the box or have you lost it?
Have you checked with your opponents?

If you play at a local store or club, Check with your local gamers.
Loads of people have spoiled decks and will be able to give you the card you're missing.
try by putting a message on the stores FB group.

Panic...

It happened during gaming. Not sure when or where, but I noticed I'm 1 card short...

I've had games where people playing next to each other, have their damage decks next to them, and they end up using their neighbor's deck! Happens more often than you'd think.

It happened during gaming. Not sure when or where, but I noticed I'm 1 card short...

I've had games where people playing next to each other, have their damage decks next to them, and they end up using their neighbor's deck! Happens more often than you'd think.

Easy fix for future is to put small coloured sticky dots on the front face of your deck, I put all mine in the bottom right hand corner. Easy to distinguish your deck from other people's (or even multiple copies of your own if you have them using different coloured dots). Use the front face as they therefore cannot be seen in normal play so shouldn't cause an issue regarding "marking" your deck. (my cards are all sleeved so the dots are on the sleeves in case anybody takes issue to the dots [no-one has to date] and I've played them in casual and tournaments...)

I also use the dots on all my dials, movement templates, asteroids and range rulers, saves any "is this yours or mine?" discussions...

Well if you are missing a Direct Hit and you played against this guy, there is good odds that he's the one with your card.

http://community.fantasyflightgames.com/index.php?/topic/133211-count-your-damage-deck/

Sharpie pen. Put your name or initials in the center of the explosion.

Count your cards after every game.

Keep your deck in one of the small zip-locks you get with every ship when not in use.

If you purchased (or know someone who purchased) extra core sets, save that damage deck.

I have my damage deck sleeved, and put my initials on the sleeves in sharpie (on the face side, not the explosion side). REALLY easy to figure out which are mine because I used green sharpie. And I habitually count out the 33 cards after every game.

I was missing a single card and contacted support.

They ended up sending me a whole new deck + some random upgrade cards.