ios 10.0.2 links open in safari not apps
I have an iPhone 6 and just upgrade to ios 10.0.2. Links connecting to apps like youtube and Instagram are opening in Safari instead of in their respective apps (like they have since at least ios 8). However, they are taking the extra step to go through the app like they are going to open there as normal, but then open in Safari. For example, if I click on an Instagram link within the description box of a youtube video Instagram opens, but then suddenly shifts to Safari once the app loads. In Safari the top left will say back to Instagram, but if I go back it is just my home feed and not the link I clicked. The link to the account I clicked on is open in safari, but that is inconvenient because I am not logged in to various accounts all the time on safari so from there I can't like, follow, share etc. The same goes for the reverse, if I click a youtube link from an Instagram profile it opens the youtube app then stutters and opens safari and if I click back to youtube in the top left it goes to my usual youtube feed and if I click open in app from safari the same thing happens (just my feed, not the video from the link). I can't find any information on this problem except for one Beta tester asking the question back in July and one other person experiencing the same thing a week ago when clicking on links in whatsapp. This really slows things down as it goes through a two step process to open the app then the link in Safari where I am not logged in. Anyone know how to fix this or how to report it?
iPhone 6, iOS 10.0.2