The party’s deputy leader was shown to have supported a Labour amendment to the Government’s Brexit motion on Wednesday night, according to the division list.
The Scottish MP’s apparent defiance of her party’s policy raised eyebrows in Westminster, but a party source said it was a “genuine mistake”.
She was the only Lib Dem MP to support the policy.
Ms Swinson has been the MP for East Dunbartonshire since regaining her seat in 2017.
Labour’s amendment called for a permanent and comprehensive customs union with the EU; dynamic alignment on rights and protections; commitments on participation in EU agencies and funding programmes; “unambiguous” agreements on the detail of future security arrangements; and close alignment with the single market.
The Lib Dems tagged their own amendment on to Mr Corbyn’s proposals, calling for an extension of Article 50 to provide time for a referendum.
Mr Corbyn’s proposals were defeated by a margin of 240 votes to 323.