There are a few reasons why you were charged more than you expected.

1. You have more listings enabled than you expected and need to disable the listings you don't want to automate.
2. If you added a new listing in the middle of the previous billing cycle you aren't charged until the next billing cycle begins.  At the beginning of the next billing cycle, you are charged the previous billing cycle's prorated charge as well as the current billing cycle's fee.  
3. You have one listing on multiple channels (Arbnb, VRBO, and Houfy) and the listings are not linked. This means that Host Tools does not know it is the same listing on multiple channels and sees it as 3 seperate listngs. Read this help article for instructions on linking listings.