If you evade tax, you know full well what you are doing, even if it's technically legal you should expect to be retrospectively taxed, especially if you are exploiting the system to such an extreme.
Oh wait, actually even the people who wrote a system for unchangeable, code-backed legal documents don't believe in the letter of the law.
There are actually limits to how far back the dodged taxes can be collected. That's why it's only $13bn. That's what has been due since 2003. This entire thing actually goes back since the 1990s.
Also, we're not even talking about criminal charges or fines here. Apple isn't being sued or facing any punishment. The EC has merely ruled that Apple didn't pay all the taxes it legally owed Ireland and Ireland didn't have the authority to allow them not to pay the taxes in the first place.
This is akin to a janitor charged with collecting rent for the landlord telling you for years that it's okay for you to pay pennies to live in your mansion until the landlord finds out about it and now demands you pay the $$$ you owe him because the janitor was never legally in a position to make that kind of deal and you're actually a highly paid expert in rental contracts and were fully aware of the deal having no legal basis to begin with.
This decision can't have been a surprise to Apple. Seeing this kind of thing coming is what they pay very expensive legal experts for. They knew EU law overruled the Irish laws that supposedly allowed this deal in the first place. They're only crying foul because they were caught.
What it looks like they are trying to do is apply a legally compliant level of taxes retroactively, not laws.
(Yeah, I know you're saying it was legal under Irish law, but the whole point is that some Irish laws take precedence over others. In this case, their treaty obligations to the EU, codified in their laws, take precedence. If this wasn't the case there wouldn't even be a court case, much less a judgement.)
That only applies to new laws.
There's a big difference. The latter is legal, the former is not.
Apple did not do anything wrong from what I can see: they were given a good deal, they took it. It turns out that deal was illegal so they have to pay some money to rectify the error.
Doesn't seem very fair but governments are pretty unforgiving when it comes to taxes overall.