1. SBF agreed (voluntarily!) to be extradited from the Bahamas to face ~X charges in the US.
2. After being extradited, he was charged with X + Y charges.
3. He claims that international extradition agreements make this illegal.
4. The judge ruled that, <citing precedent>, international extradition agreements allow the Bahamas to raise a complaint about this - but does not allow SBF to do so [1].
5. US prosecutors have expressed that they are willing to drop the Y charges if the Bahamas raises a complaint in a timely fashion.
6. The Bahamas are incredibly unlikely to raise a complaint on this point.
tl;dr - Expensive lawyers can force government prosecutors to dot all their is and cross their ts, but if they have you dead to rights, you're still screwed. SBF seems really, really screwed.
[1] These parts of extradition treaties are generally very explicitly about the rights of countries, not the rights of individuals.