Parliamentary sovereignty was applied in approving the referendum in the first place. The referendum took place at the direction of an Act of Parliament. That should be quite sufficient to establish that the govt applying the result of the referendum is under the umbrella of Parliamentary sovereignty.
This is just a b.s. attempt to drive a wedge into the process, hoping to overturn the result of the referendum.
Parliament did indeed authorise the referendum. What it did not do was the authorise the Government to implement the result of that referendum in whatever way it chose, without further reference back to Parliament. And since one of the core purposes of Brexit is to reassert the sovereignty of the British Parliament over any body, the judgement is reconfirming the people’s will, not contradicting it.