So we shouldn't catch criminals then. By that logic, investigations, and evidence gathering for said investigations is not right either.

There are very good reasons for evidence obtained by unlawful means to be ignored, even if it would help to catch a criminal.

I never understood why that's the case. Is it not to encourage unlawful activity?

Stealing an example from mr robot, if I break into someone's computer and find evidence that proves they are trafficking underage photos, I don't see why that proof should be ignored , in any circumstances.

Sure, charge me as well with breaking into someone's computer, if you can catch me, but don't dismiss my evidence.

It is to discourage unlawful activity on the part of law enforcement.

Sure, and that's probably best. In my original comment, I specifically mentioned that what the FBI is asking for is reasonable providing there is a warrant, which would imply that they're gathering evidence lawfully.

I think the main problem is that we allow the justice system to step on private companies.

I think the company owning the data should be able to decide whether to give the data and aid the investigation or not (which is something that affect their reputation and that they can tell their customers, either as an advantage or a disadvantage)

I prefer to have clearly identified and clearly limited exceptions to my rights, rather than a large scale violation of our rights, hidden with lies.

That is true, but it does not follow that all reasonable cases will develop into egregious ones...