iOS 9.3 had a big problem with processing universal inks which caused any links in apps to break. If you’re hit with the problem do a software update now.
Now iOS 9.3.1 is out it gives the shared web credentials daemon (swcd) enough memory to process large association files, and recover from previously large files that had previously pushed swcd over the limit.
Expect to see a future update to iOS limit the maximum size of an apple-app-site-association file to be something more sensible than unlimited, like 128 Kb.