One possibility is to have a looser flat file schema, that will parse data that is invalid, lots of optional records and fields and then have a subsequent check. Map into a stricter schema possibly or use a Schematron type validation in an orchestration using a map.
Can you go back to the source and correct the reason for the problem there. Ensuring only good data is sent.
If the source is external, then I find automatically rejecting errors back to the source can focus the sender into correcting their mistakes