"Sorry to bother you" in an email?
I think that @ndpl hit the nail on the head when he commented that what's most important is that your message to the professor be clear and concise. 

During an academic semester I, like most academics, get a crazy number of emails. (I'm an assistant professor of mathematics at a college in the US.) If your email is short and to the point then chances are I'll be able to read it right away, decide what action on my part needs to be taken (if any), and move on to the next email. Empty statements like "I'm sorry to bother you." are polite, but just make my goal of getting through all the unread messages in my inbox that much harder to achieve. 

So if your email was written in a professional manner, but was just terse, that's absolutely fine.