Yes but it isn't a Gibraltarian ship.
This really really is not a difficult concept. The ship is Iranian, as an Iranian ship neither it nor its operators have to comply with EU sanctions on Syria, therefore it did not break EU law by not complying with the sanctions it was not required to comply with.
No, you're getting this completely confused it is a Panamanian flagged ship owned by a company based in Singapore. The ship or the cargo might ultimately be owned by Iran but it is a civilian ship and it isn't exempt from the law!
You've again avoided answering the questions posed previously about fishing... funny that... the basis for your claim is complete bunk essentially - flying a flag of another country doesn't exempt a civilian/merchant ship from the laws of the nation whose waters it enters (aside from international rules relating to free passage in certain areas).
The fact it was sailing in EU waters is not relevant because the EU does not enforce it's sanctions like the USA does (I.E "sailing towards Cuba with supplies, we have sanctions on them, turn around or get sunk"). It did not break EU laws, because the law doesn't require the vessels of non-EU states to comply with sanctions that only apply to EU-members and their vessels, even if sailing in EU waters.
Yes it does, that is literally the legal basis for the stop, Gibraltar is part of the EU and EU law applies there. Why do you think the Judge approved the stop?
If the ship didn't want to adhere to EU rules then it shouldn't have planned to stop in Gibraltar. honestly you're just talking complete BS here and have provided nothing at all to back up your statement other than some stupid flow diagram you drew... on the other hand others have referred to the relevant rules that the ship has been seized which have also been confirmed by the government of Gibraltar.
If they've not in fact broken EU law or it doesn't apply then they're perfectly free to challenge it in court - though seemingly the current claim is that they weren't actually sailing to Syria (after taking the long way around) and if that is the case (and they can provide assurances) then the UK was prepared to release the ship anyway.