How can I alert Apple about spyware targetting Apple users? I got a pop-up on my father's iPhone stating that there was spyware on it, along with a number to call for AppleCare support. I realized I only called the number because it was listed in a pop-up and wasn't really sure if it was really AppleCare. I looked up the number on my other phone and discovered it was a scam.

How can I report this to Apple?
For what it's worth you can reach Apple's legal department through the contact form on https://www.apple.com/legal/contact/. Picking "Phishing and Spam" from the drop-down leads you to https://support.apple.com/HT204759 which, among a lot of useful info on how to protect your devices, lists a number of options on how to reach out to Apple in these cases.