How can customers know why local pick up isn't available?

I have two locations set up for pick up. One location has 5 bags and the other has the T-shirt. The delivery says pickup isn’t available because if you buy a Shirt and a Bag and one location doesn’t have both it just says pick up isn’t available.

Is there a way for customers to know why pick up isn’t available?

You could try editing the theme language, to say something like “1 of the items in you order isn’t available for pickup, please contact us at …”

How to edit theme language: https://help.shopify.com/en/manual/online-store/themes/customizing-themes/language/change-wording

In your case you could search for something like “pickup” to try and find the phrasing they use, then adjust that with your new custom phrase.