Stupidly, because it was a rush to the deadline, my electronic submission (TurnItIn) had an old version of the contents page with incorrect page numbers. I'm pretty sure they only use that as a tool for checking for plagiarism though- they actually mark the hard copies (which were fine).
You'll be fine, it's the hard copy they usually mark. I'd drop your department administrator/exams office a note to say that the printed version is correct, but you submitted the wrong one electronically as Tudor suggested.
I actually did the opposite for my MSc. Printed and submitted the old copy, which included lots of "notes to self" and things I meant to have time to go back and fix in the text. The electronic copy was the one I meant to print and submit, but I was so close to the end and a friend was bothering me when I sent the work to the printer I didn't notice it was the wrong version.
They marked the hard copy, including all those comments to myself. Cost me my distinction in my MSc (I averaged >85% but my project was only marked at 68%) so I was only awarded a pass. I'm still bitter about it 6 years later... Sigh. Lesson definitely learned though!