The party has sought an explanation from two of its leaders over their comments on social media opposing Mr Siddiqui's entry.
"The Uttar Pradesh Congress Committee considers as indiscipline the views in the party opposing the joining of Mr Naseemuddin Siddiqui and others on Facebook," a party release issued read.
Member of the disciplinary committee Fazle Masood sought an explanation from party's organising secretary Sanjay Dixit and secretary Avdhesh Singh in this regard, it read.
Party sources said Mr Dixit, in a series of Facebook posts, had opposed the entry of Mr Siddiqui in the Congress.
He accused UP Congress leaders of misleading party president Rahul Gandhi in this regard, they claimed.
"Siddiqui has been synonymous with all major scams during the Mayawati government and had been her right-hand man ... How can a tainted leader like him be permitted in the party when Rahul Gandhi is advocating clean politics," Mr Dixit wrote on Facebook.
When contacted, Mr Dixit said he would personally meet Congress president and apprise him of the reality.
Mr Singh is said to have opposed Mr Siddiqui's joining on the ground that he had made derogatory remarks against the Thakur community during a BSP agitation in Lucknow.
In July 2016 during an agitation against derogatory references made by a BJP leader against Mayawati, Mr Siddiqui had allegedly made remarks against a 12 year-old daughter of the leader who is a Thakur.
Mr Siddiqui had formally joined the Congress in New Delhi earlier this week.
Once considered the Muslim face of the Mayawati-led party, he was expelled last year for alleged anti-party activities.