In the absence of a clear report from the police, the regional passport office (RPO) may summon you and in such a case, you'll to appear before passport officials to explain the point on which the police submitted an adverse report.
You need not be worried with this. You can continue to use your fresh passport. At anytime you receive a summon from RPO, you may either appear in person or send your explanation through a registered post. If the RPO finds your explanation sufficient, he'll reinitiate Police Verification.
For now, you may get your passport stamped and you needn't worry for you haven't indulged in an act of fraud or misrepresentation.