Send out the invoice.
You are in business and deserve to be paid for any work you do. Your time spent on their work is time you could have spent on someone elses and been paid for it.

If a plumber came to your house and you didnt like the look of him, maybe he smelled, dawdled and took all day to do the job you would decide not to use him for future plumbing work but you would still pay for the work done.

Web development is like any other business. At the end of the day it is business. Be firm and get what is owed to you.