The SNP suffered its worst day in government yesterday, culminating in a humiliating climbdown on the thorny issue of whether an independent Scotland would automatically remain a member of the EU.

For months the Nationalists have attempted to close down debate on the issue by insisting it was done and dusted. Unexpectedly yesterday, Deputy First Minister Nicola Sturgeon revealed no specific legal advice had been sought.

If this is the case, taxpayers are entitled to know why the Government has spent £12,000 of public funds going to the Court of Session in an attempt to prevent the publication of whether or not such advice had been sought. They would also like to know why the First Minister appeared to give the clear impression in a television interview in March that reassuring legal advice on this issue had been obtained. Alex Salmond has questions to answer.

It merely adds to the sense of drift engendered by the ongoing row about the Electoral Commission's rules about funding for the independence campaign. In a separate development, yesterday saw the much-delayed publication of the consultation on the independence referendum, more than a week after the fundamentals of the exercise were signed and sealed by Mr Salmond and David Cameron. So much for "a listening Government".

Then there were the Nato rebels. It was Victorian Prime Minister Benjamin Disraeli who first proffered the advice: "Damn your principles! Stick to your party." Highland MSPs John Finnie and Jean Urquhart beg to differ. Yesterday they both opted to resign from the SNP over the party's decision to end its traditional opposition to Nato.

The move will make precious little difference to the Scottish Government's political arithmetic because both of them will continue to support the SNP Government on the vast majority of issues and, as defence is currently a reserved matter, the subject is unlikely to crop up at Holyrood any time soon. Also, though this is the first substantial revolt suffered by Mr Salmond's administration, the rebellion offers limited political capital to Labour, which is itself unclear about its attitude towards the UK's so-called independent nuclear deterrent. At the same time, while barely a crack was allowed to manifest itself in Mr Salmond's ranks, it was easy for the First Minister to depict his rivals as riven by divisions. That will now be more difficult.

The passion displayed in the Nato debate at the SNP's annual conference revealed deep divisions on the issue and the margin of victory for the leadership was not wide. The case for abandoning the SNP's traditional hostility to the Nato alliance was largely based on pragmatism: it was less about what is morally right than dismantling a perceived obstacle on the road to independence.

By contrast, Mr Finnie and Ms Urquhart can justifiably claim they are sticking to the platform on which they were elected and point out that it is the Scottish Government that has changed course.

Nevertheless, it makes a nonsense of the list system that two MSPs, both elected on party lists, can hold on to their seats and their salaries, despite deserting the party. If they are no longer party members, however limited their rebellion, logic should dictate they resign and join Margo MacDonald by standing as independents. As things stand, though the SNP still enjoys an overall majority, it has lost four of its 69 MSPs, including Tricia Marwick, who became Presiding Officer, and Bill Walker, suspended over domestic abuse allegations.

Added to the revelations about non-existent legal advice, yesterday was Mr Salmond's darkest day since he came to power. And future potential fractures, in particular between the economically liberal and socially liberal wings of his party, could be even more damaging. The SNP's case for independence rests largely on the administration's competence and confidence. It would be premature to say these have been undermined by recent events but they have certainly been shaken.