But Tory Nigel Evans told the US president's critics to "get over it" and that plans would not be changed.
The debate was triggered by two petitions - one against a state visit, which got 1.85 million signatures, and one in favour which got 311,000.
Opening proceedings in Westminster Hall, Mr Flynn, a member of the petitions committee, said it was "extraordinary" an invitation had been issued so soon into the US president's term.
He said there was "no question of any disrespect" towards the United States in opposing Mr Trump's visit, but said the president had caused problems in "every political area in which he has become involved in" and had been " behaving like a petulant child".
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