In case of such force majeure that prevents you from leaving the Schengen Area within the validity period, you should contact the border authorities in the country you're in ASAP to get your visa extended with the time you need to leave.
See the Schengen visa code, article 33.1:
- The period of validity and/or the duration of stay of an issued visa shall be extended where the competent authority of a Member State considers that a visa holder has provided proof of force majeure or humanitarian reasons preventing him from leaving the territory of the Member States before the expiry of the period of validity of or the duration of stay authorised by the visa. Such an extension shall be granted free of charge.
The visa code handbook (section V.1.1) explicitly mentions "last minute change of flight schedule by airline" as one example of force majeure.