In ‘Dragon Age’, what are “doubles?”

The intention is at least two out of three dice showing the same face.

First of all, the Ability Tests section on page 46 makes clear that when making an ability test, your final result absolutely includes the Dragon Die (emphasis mine):

To make an ability test, first pick up three six-sided dice (3d6). Two of the dice should be one color and the third a different color. The off-color die is known as the Dragon Die (see The Dragon Die sidebar on page 47). Roll all three dice and add the results together; you want to roll high. You then add the ability you’re testing and another 2 if you have an applicable ability focus. The final number is your test result.

TEST RESULT = 3d6 + ABILITY + FOCUS

The Combat Stunts section on page 54 of the Dragon Age Core Rulebook states (emphasis mine):

The stunt system is simple. If you make a successful attack roll and get doubles on any of the dice, you can perform one or more stunts in addition to dealing your normal damage.

This is consistent with the worked example on the following page:

… Her test result is an 18 in total and her dice read 3, 5, and 5, with one of the 5s being her Dragon Die. This beats the tough’s Defense so Jannelle hits. Since she also rolled doubles, she receives a number of stunt points equal to her Dragon Die (5 in this case)…

And with a much later non-combat example regarding roleplaying/exploration stunts on page 132:

… Gerhard has Communication 2 and possesses the Investigation focus. He rolls 4, 3, and 3, with the 4 being the Dragon Die result. His total is thus 14, which exceeds the target number. The GM tells the player that Gerhard was successful. Since doubles were rolled, the test generates stunt points equal to the Dragon Die result of 4…

Which makes clear that the double can be on any two of the dice and it doesn’t matter if one of them is the dragon die or not (at least for determining if a double has been rolled).

It appears you feel that this cannot be intended because that would generate stunt points too frequently. However, the DA system expects that you will regularly be generating stunt points. Much of the interesting stuff you can actually do in the system requires stunt points and many of the class abilities are based on reducing the cost of certain stunts to support a specific playstyle. This is not directly equivalent to getting a critical hit in D&D or similar games; stunts should be common. Remember that even if you do generate stunt points, the number is still variable – what you are able to do ranges from very minor (for instance, being able to move a bit further or push your opponent) to striking a Lethal Blow (which is more of a critical hit equivalent).