i believe iOS 9.3 introduced slightly different lookup logic around the apple-app-site-association file and the app handoff feature.
“Handoff first searches for the file in the .well-known subdirectory (for example, https://example.com/.well-known/apple-app-site-association), falling back to the top-level domain if you don’t use the .well-known subdirectory.”
see: https://developer.apple.com/library/ios/documentation/UserExperience/Conceptual/Handoff/AdoptingHandoff/AdoptingHandoff.html#//apple_ref/doc/uid/TP40014338-CH2-SW10