I just checked my server logs and found the following weird requests coming in quite a lot. I have iOS 9 Universal Linking implemented, but those requests are running against /apple-app-site-association as far as I know.
Jan 15 09:36:23 method=GET path="/.well-known/apple-app-site-association"
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."