I am not familiar with medical FSAs, but here's how it worked for the dependent care account when we inadvertently doubled up on our election. Since we actually spent more than we had withheld, we each were able to submit dependent care expenses and retrieve the funds back from our employers during the course of the year. At tax time (we used turbotax), the amount over and above the allowable withholding was simply added back to line 7 of our 1040 with a 'DCB' coded added to the line. There was no penalty I don't think, other than having to pay taxes on the excess over the limit (which makes logical sense).
I'm not 100% sure we handled it right, but I was fairly comfortable with it based on the research I did on it at the time. Again, dependent care has different rules than medical, but maybe this is helpful to you. This of course is not the advice of a professional.