If you own a small business that provides online booking facilities to your customers, the chances are pretty high that you're using another company to provide those booking services for you. Visitors to your site click on the "Book Now" link and this takes them to a managed page on the booking company's own site where they complete their booking. It's convenient for you because you don't have to pay a developer to build one for you and it can be ready to go in a matter of hours.
However, there can be serious drawbacks to using this kind of "external" booking engine.
What else can go wrong?
The more "intangible" argument against these third party bookings is in the user experience. Today's web users are generally far more "web-savvy" than they have ever been and links that cause a redirect to a new domain or - worse - a pop-up window are mis-trusted. It won't scare everyone off - such booking tools are common enough that most people will expect this behaviour - but if it affects just 10% of your potential customers, it could amount to a fair sum.
This supposition can be made more "tangible" of course if you are able to examine Analytics to determine a "bail-out" point but if you can't get the code in there...
If you used an external booking engine as a method of saving on the cost of your own site, consider how much custom you may be losing from that decision.
While we're on the subject of cost, consider the charges levied by these booking engines. Typically they'll charge a percentage of the booked sum (although there are some who use fixed charges either per transaction or per period). If you used a third party engine to save on web-development costs, have you worked out how long it would take to recover those costs in savings? Perhaps you'll find the "internal" option would have paid for itself long ago...
Think long-term about costs. External booking engines charge forever, your own (normally) will only charge once.
I'm not against external booking engines, some are very good - Sabre Hospitality for example provides just about every customisation option under the Sun (including CSS, HTML, Adwords, etc.) - but others don't come anywhere close. When looking at these engines, think hard about the options before making a choice.