I read somewhere that the Dark Matter drop rate is 25% but I'm convinced that it's 12.5%, that figure is more correct according to my drop rates. Also, Dark Matters for Break Damage Limit is an utter waste of them, get the Ultimate Weapons and save the Dark Matters for Ribbon. Anyway...to get Dark Matters I fight Sleep Spouts if you can defeat them they are very useful to fight because;

1, They drop Teleport Spheres, which can be used to raise stats very effectively.
2, You can take them down in one hit, out of all the monsters in the Arena this is the quickest to kill for Dark Matters.
3, It Drops equipment that you can sell for lots of gil, if you keep defeating it until all your money has gone, sell all the equipment it dropped and you will find that you now have more than double the amount you had before you started fighting it.
4, It gives a decent amount of SP (Not the best reason to fight it but nonetheless this shouldn't be over looked)
5, And of course they drop Dark Matters just as well as anything else.

Sleep Sprout have 95000HP so if you get Aurons Ultimate weapon, Face Sleep Sprout, then die then face it again without going to the Save point you should be able to defeat it in one fell swoop (If not raise Aurons Strength then try this again).