You should always ask for an estimate on how many hours any job will take and how much it will cost (ask for a max if you need to in order to get a cap) when you have them do work. At all times you should know how much any of their jobs will take. To protect yourself in the future you can also say that for anything costing over $X you need to have written approval by the CEO/CFO before they can start the work, they will complain about it, but you can always play it off as establishing internal controls in the company. If you've done the above and if something is wrong, talk to them, they are usually reasonable people. Customer service is a part of their business.
In your particular case, I'd recommend asking to split the payments over time. They may ask for interest, but at least it will help your cash flow. Keep in mind, they want to make you happy now - You just got funded and are a growing company. They want you to stick around and be their client as you grow into a billion dollar business, not have you leave to a competitor over a $40k+ bill. It's almost trivial when compared to a long term business relationship.
edit: What's the worst that can happen? They say no and you pay the bill.
Hope that helps!