But Scottish Brexit minister Michael Russell said parliament needed "to unite to protect the powers of devolution".
But the Tories hit out, claiming it was "patently obvious that Nicola Sturgeon wants a political crisis to provide cover for her independence drive".
Scottish ministers contend that the devolved parliaments should have to give express consent for changes to these frameworks, while the United Kingdom side argues that this would effectively give MSPs the power of veto over frameworks extending right across the country.
"The amendments themselves are extremely problematic because of the definition of a consent decision, which effectively means that if the Scottish Parliament votes to refuse consent, the United Kingdom government can in effect take that as a "green light" to act anyway", the source added.More news: Sadr eyes Govt as poll upset rocks Iraq
Mr Russell added: "The Parliament will vote to reject legislative consent for the Withdrawal Bill - not just the Scottish National Party in government, I think all the parties save the Conservatives will actually vote for that".
May is trying to strike a trade deal with the European Union by October while at the same time negotiating with her party and senior members of her divided minority government over Brexit.
Months of negotiations has seen some agreement, and the Scottish Government are happy with the idea of common frameworks, but as long as Holyrood has the ability to accept or reject them.
Labour's Neil Findlay said there was still time to fix the bill.
The UK Government has balked at this on around 24 of the powers being repatriated from Brussels, unwilling to give MSPs an effective veto.
"The UK government can not ignore the reality of devolution or try to drown out what this parliament says", he said.More news: Arsene Wenger claims he nearly signed Cristiano Ronaldo
"There is a clear solution which is, as I have said and as the committee agreed last week, to simply remove [clause 15] from the bill".
Scottish Greens co-convener Patrick Harvie said MSPs needed to stand against Theresa May and Ruth Davidson's "devolution demolition squad".
"They have a decision to make as to whether they are going to ignore the views of the Scottish parliament or listen to those views and try very hard to get a deal and to close the gap that remains between us".
MSP Adam Tomkins, the party's constitution spokesman at Holyrood, insisted: "A deal is there to be done on Brexit".More news: Coroner: Detained suspect in Louisiana died of asphyxiation
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