What do I do if my dad's I485 application was rejected saying it was misfiled?

The USCIS sometimes errs in its analysis of a case, including its determination about proper filing; additionally, applicants often misunderstand the sometimes complicated laws, regulations and court decisions that dictate proper preparation and filing of a case - the applicable rules can be more complex than they appear. There really is no substitute for working with an immigration attorney who, from the onset, could assure eligibility for the benefits sought, and who could provide legal assistance in assuring that each application is properly prepared, fully documented, properly filed and appropriately adjudicated by the USCIS. Some immigration law firms, including mine, offer legal services on a "flat fee" basis so that a client will know the total expense from the very beginning, and a few immigration law firms, including mine, offer an initial consultation free of charge.

It depends on the precise reason, but you should be able to refile.