Hi,
How can you tell if the site was caching too aggressively.
For example, take the first URL in your CSV file:
https://www.beeswaxcandleshop.com/store/beeswax-decorative-animal-figurines/product/updatecart/add-1/cid-218.html
Suppose that you open it on a browser which you don't normally use to access your website, or in incognito mode.
This will add the product with the id 218 (you can see it at the end of the URL) to the cart and redirect you to the checkout at
https://www.beeswaxcandleshop.com/store/beeswax-decorative-animal-figurines/checkout.html
In the cart display on that page, you'll see the product with a quantity of "1" in the cart.
Now, if you open a new tab in the same browser window and access this same URL again, it will again add the same product to the cart and redirect you to the checkout.
So, on that new tab, you should now see the product in the cart with a quantity of "2".
If you still see a quantity of "1" in the cart, it likely means there is a page caching issue as you're actually see the page that was generated before, on the first try, instead of the new page content.
What you can then do is to add an extra parameter to the URL in the browser's address bar.
For example:
https://www.beeswaxcandleshop.com/store/beeswax-decorative-animal-figurines/checkout.html?myextraparameter
You can change myextraparameter by something else. Since the URL is different, the page caching mechanism will force the regeneration of the HTML and you should then see the proper quantity in the cart.
And if you then access again the URL of the checkout without the extra parameter, you'll see again the cached URL with the wrong quantity.
Now that you've turned off the cache on your website, I'm not able to reproduce the problem anymore. I properly see the correct quantity of the product in the cart whatever I do. So that's good.
most all of the files listed were old cart files that should not even have been visible
I'm not sure what you mean. If you want a product to not be visible anymore on the frontend, you need to unpublish it. This will result in its URL generating a 404 error on the frontend since the product is not there anymore. This is normal and what it should be.
The problem with SEO would be if the URL to a product page or an add to cart page would result in a 404 error even though the product should still be visible on the frontend. I couldn't find an example of this on your website.
The CSV you got seems completely unreliable. I will be hard to draw any conclusion from this.