The only condition when I can think not to take a card is if another player is going to knock you out and use those cards to run the table. But seeing how you'll be out of the games, I'm not sure it's worth worrying about. The only other condition I can see is if you are at a stalemate with another player (say at Australia on the original map, with just one entry to the continent). If you take a territory, then they can have an easier time of taking a territory and collecting a card. So in effect, not taking a card could be a strategic move to keep another player from building up. Odds are this is more of an end game issue and not likely to be an issue at all. Lastly it might not be a great idea to take a territory to get a card if you have to spread yourself too thin but that goes more to strategy. On that same note, maybe you're too thinned out already and can't take a territory and therefore a card. So general rule of thumb I'd say it would usually be best to take a territory/card if you can.
SectaOne