Right, but there are also legitimate problems with Amnesty too. It admits itself that it tends more towards criticism of state actors and typically western states because it feels it's safer to investigate them and easier to acquire the information to investigate. You can see Amnesty's own admission of this here, though the cited link doesn't seem to work any more:
What this typically means is that say, Hamas can fire rockets specifically with the aim of killing Israeli civilians by targetting Israeli cities and avoid criticism, whilst if Israel responds and hits the rocket launch sites killing a civilian accidentally as collateral damage then Israel will receive a scathing response from AI. Now I'm not trying to comment on the Israel/Palestine conflict here, Israel most definitely does have plenty to answer for, but I am citing this as an example of the issue because it's truthful and legitimate.
It's also somewhat understandable, because it's far safer for Amnesty investigators to investigate somewhere like the US, or the state of Israel, than it is to investigate Hamas or ISIS but on the same note inevitably what this means is that Amnesty ends up attracting people with deep anti-Western sentiment, because this bias ends up giving the impression to many that they are an anti-Western organisation.
It shouldn't be surprising then that Amnesty does start defending questionable cases sometimes, and that as a result they attract questionable people to have in their organisation - some people may wish to investigate a state like Israel, not because they believe in general justice, but because they see it as an opportunity to politically attack Israel whilst believing it's okay what Hamas does even though Hamas is similarly guilty of the sorts of gross human rights breaches that Amnesty is meant to argue against.
Now, at the end of the day, this surveillance of Amnesty was deemed to be unlawful, and the fact therefore that it was illegal is in itself enough for me to agree that this was unacceptable and wrong. But I can see why at least some segments of Amnesty might reasonably be classed as a legitimate surveillance target for Western intelligence agencies with some of the people it attracts. What makes it incredibly awkward though is that due to Amnesty's size, you may well find that whilst it's justifiable that Western intelligence targets some of it's members, other members are legitimately investigating those very Western intelligence agencies, and that creates a hell of a mess, because it's unlikely that those intelligence agencies could stop themselves from just snooping a little more past simply legitimate targets at Amnesty and on to non-legitimate targets who are rightfully investigating them.
I don't know what the solution is other than Amnesty to clean house, and be more objective so that Western intelligence doesn't have any legitimate reason to spy on them in the first place. That solution feels wrong, as it feels somewhat like victim blaming, and an awful lot like the if you have nothing to hide fallacy, but what else do we do when Amnesty does have legitimate surveillance targets working with it? Are there organisations like Amnesty that should always be out of bounds regardless of who works for them and who they might be supporting and helping and what they might be planning with them? I'm not even going to try and pretend I know the answer to that question.
It all gets very messy and creates many shades of grey when you've got two far from squeaky clean organisations going at each other.