You may want to point this out to management the next time you go. You may also ask them if they have any ketchup to go when you pick up your order, even if you don't take it to go. They probably have to fill it from a different container or give you little packets. That way you don't have to use the bottles if they gross you out.
The fries were perfect and cheap! We too noticed that some of the ketchup bottles needed to be refreshed.
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