Ah, it’s not really built for multiple vaults—it just activates Obsidian, which means your most recent vault will be the one it grabs.
There should be ways of customizing that, though, especially with the new obsidian://open? and obsidian://search? URL schemes.
How many vaults do you have? If it’s only a couple, your best bet is probably to differentiate the Alfred command to use different obsidian://open?vault=VAULTNAME actions depending on which vault you’re targeting. E.g., if you type work some note, treat work as the keyword trigger for your work vault and some note as the query.