Is it normal to take costs such as a plumbing repair out of the rent?

My gf thinks that we have commited some crime and is attacking me like crazy because we had a plumbing problem, and the landlord said to just take care of it, and take it out of the rent, which isnt a problem at all. Am I really wrong in doing this? The Plumbing issue was a simple drain clog that required the plumber to drill a small hole into the offending pipe in order to get to the clog. Landlord knows he is responsible.