Did you take our class? If so (and if you haven't already done this), then you're eligible for a free Post-Exam Assessment. This is a phone call with an instructor to figure out what went wrong and come up with a plan to re-take the test. If this applies to you, please send an email to
studentservices@manhattangmat.com and request the Post-Exam Assessment right away - this is the best feedback you can get!
You did fill in all of the remaining questions? Your penalty would likely have been something like 10 to 25 percentile points for that section (depending upon how many you happened to get right and how many were experimental). If you left some questions blank, the penalty would be at the higher end of that range.
So, yes, that's a pretty significant penalty. If you can fix the timing problem, your score would likely be higher on a re-take - I don't know exactly how much, though.
Were you taking practice exams under 100% official conditions, including essays and length of breaks? If you deviated from official conditions in any way, let me know how. (That can result in artificial score inflation, so that would mean your practice test scores weren't as high as you thought.)