My non-kashrus-professional take on this:
A place like Costco could very well be selling a bulk pack of items from multiple productions. As the hechsher is still relatively new it could be some of the bottles were from a pre-hechsher run and are indeed NOT kosher. Check this by looking at the “use by date” – my guess is that the non-hechsher ones are quite a bit older than the hechsher ones. Kudos to you for noticing it!