If someone RSVPs with an unexpected additional guest, it is your choice as to how to proceed. Generally, it's best to set some guidelines when making your guest list and to stick to them as much as possible. The more exceptions you make, the more you might open yourself up to rude questions from other guests. If you only receive a couple of additional RSVPs, and you don't want to make a big deal out of it, then that's fine. However, if you wish, you are well within your rights to call the guest with the uninvited "plus-one" and give any number of explanations regarding the firm head count (reception venue size, catering estimates, etc.). Unless the plus-one is the invited guest's live-in partner, fiancé, or spouse, in which case it was your error, not theirs.
For more guest list-related questions: