Yes.
In Pakistan every Tim Dick and Harry illegal can live for a long time. Millions of Afghans living in Pakistan for years, getting Pakistani passports and ID cards, and even traveling as illegals on Pakistani documents. So a few Indians using Iranian documents to hurt Pakistan is not enough proof of Iranian complicity. And I see no reason Iran would like to open a front against Pakistan, border skirmishes and loud-mouth Iranian threats notwithstanding.
Heck, even now in America, a very regulated and monitored state since 9/11, there are illegals with fake documents doing all kinds of things.
You just don't make a hostile strategic posture based on pinpricks! Look at the long Pakistan-Iran border: Does it look like that of two hostile countries? I don't think so. In fact, had it not been the fear of the reprisals from Pakistan's benefactor Arab countries, I bet Pakistani officials would sound more pro-Iranian than they do now.