Subcontractors can bring their contract claims against the government by using the same Contract Disputes Act process.  It has a routine flow through claim sponsorship agreement with the prime contractor, and then it simply prosecutes the claim like any other litigant.

It is a commonly held belief that there are standard terms and conditions that contractors must include in all subcontracts, and that subcontractors must accept.  This is, in fact, largely untrue.  Very few clauses must be included in a subcontract and most of those deal with clean water, non-discrimination and other socio-economic issues.  Those clauses impose obligations that are required by federal law in any event, so it does not matter whether the clause is included or not.