How many words did it cut off? Why did you submit it if you went over?
In any case, last year when the AMCAS program turned all of my apostrophes and commas into question marks I printed out a good copy of my personal statement and sent one to each school I applied to along with a short letter explaining what the AMCAS program did to my personal statement. At most interviews they acknowledged that the amcas application did that to a lot of people's personal statement and they just overlook it. However, you went over the 5300 character limit. I don't think it will be that big of a deal but it doesn't make you look that great. I would send a full copy of the personal statement to each school you are applying to.