If a product stock is decreased to 0 while being in a cart, and you navigate to checkout you will get a pop-up saying it is not available any more (which makes sense):
Thank you for reaching out to the Community. To gather a bit more information, are you using any apps for your pop-ups?
If you haven’t done so already, I’d encourage you to connect with us directly. This will allow our support team to get you authenticated, as we wouldn’t have access to any account details here through the Community. They will be able to take a closer look into that pop-up to determine whether it can be disabled.
Please let me know if you have any other questions.
I am not using any apps for the pop ups, I believe they are out-of-the-box functionality from Shopify? And if so, I am wondering if it is a bug or it is on purpose the pop up is shown again.