that's the point of Bethesda games, some options mean you can't get certain loot, perks or weapons;you can mess up and fail stuff. if you really want to gather every magazine/collectible you might want to look through an area very carefully before leaving it if you know or not that you can come back. if it really bugs you and your on PC you can add the perk with the proper console command. also not Bethesda's fault for you choosing to not pick that magazine up when you could have gotten it.
Yup..just like in FO3...the bobblehead in your dad's office at the beginning and the one at raven rock are unattainable if you miss them..