You're right of course, and we certainly don't have (unfortunately, in my opinion) anything like the degree of separation of powers inherent in the US system, which was pretty much designed from the ground up with that as a central tenet of the whole edifice of State.
Parliament is supreme. Well, sort of. It lacks supremacy in a number of areas where it has ceded power to various EU or European bodies by trwaty. But in general, yes. And my terminology was a bit loose too. Parliament makes laws, yes, but of course, judges interpret them, and that gives quite lot of scope. And then, of course, if law A says this, but law B says that, and the two overlap or even directly conflict, it'll be judges that degermibe which overrides which, in that case. And perhaps I should have said "regulation" rather than legislation. That seems to be where 'government' periodically comes unstuck, where ministers (or Seceetaries of State, at least) implement changes to laws, or new aspects to laws, by means of authority granted to them to do so, via Statutory Instrument, by enabling primary legislation. Parliament is then still effectively supeeme, because IT passed the primary legislation authorising some future minister to act in a way not subsequently requiring full Parliamentary process.
On the one hand, it bypasses that full process, as wouldcbe required for the normal passage of an Act. On the other hand, it's an effective administrative shortcut to not tie the Commons up in never-ending fine administrative detail. It is, in my opinion, therefore both dangerous, and absolutely necessary.
The Minister (or Sec of State) can therefore act, purportedly within that authority, but in a way courts later deem to have been illegal (as in this case) effectively "striking down" the legis.... sorry, regulation, because of errors in process.
The Minister can then go back, redo it, follow process and have another go. Or of course, Parliament can exercise it's authority with primary legislation.
The check in the system, if you like, is in that Parliament makes laws but courts interpret them, and try to determine what legislation says, and what the intent of Parliament was (that not always been entirely obvious), and that where ministers exercise authority almost unilaterally, they still folliw due process in doing do.