Complete Adventurer has rules for small alchemical capsules that hold "small amount of an alchemical substance" or "one dose of any contact poison or ingested poison". Does this mean they could also be used to hold a single potion?
Potions, poisons, and alchemical items are three separate categories. Nothing that applies to one automatically applies to any of the others. If the alchemical capsule was supposed to work with potions, potions would be listed.
Why they should work with alchemy or poisons, but not potions, is entirely unaddressed by the description. It might be that a dose of poison or alchemy is simply smaller than a dose of potion. Or perhaps something about them interferes with magic—alchemical items and poisons are typically not magical (though the fact that the alchemical capsules don’t interfere with the alchemy or poisons that are magical suggests this isn’t the answer). But maybe it’s the particular way in which magic is suspended in liquid for potions, that isn’t true of alchemy or poisons made from liquids that are themselves magical. Or something else entirely. Wizards of the Coast decided not to include that detail. That leaves it up to the DM to decide. And maybe he decides there is no good reason it shouldn’t work, and allows potions as a houserule.