Don't have this problem, but had transactions being rejected before (albeit and fortunately rarely so).
Usually you can call visa/mastercard/whomever _before_ the transaction and give them an explicit waiver. Sometimes you have to ensure to have all the details of the amount and company charging, sometimes they're ok with just a quick notice to let through "anything below a hundred dollar for a day or two". But if we're talking about a distinct company and charging to a credit card, you should be able to give your credit card company a waiver from their checks for that particular company, so all the company's charges go through. Don't know if you want to give them that much freedom, though...
Usually you can call visa/mastercard/whomever _before_ the transaction and give them an explicit waiver. Sometimes you have to ensure to have all the details of the amount and company charging, sometimes they're ok with just a quick notice to let through "anything below a hundred dollar for a day or two". But if we're talking about a distinct company and charging to a credit card, you should be able to give your credit card company a waiver from their checks for that particular company, so all the company's charges go through. Don't know if you want to give them that much freedom, though...