How to know from which number a missed call came, if the caller has multiple numbers? In iOS 8.4.1, if a caller who has 6 numbers, calls you and you see a missed call. Then, clicking the "i" symbol next to the missed call showed you all the 6 numbers of the caller and the number from which he called, was indicated with blue. This helped in knowing exactly what number he called me from and I could call back on the same number.

iOS 9.0.1 call log does not indicate the number the caller called from with blue (if the caller has more than one number). So, it becomes impossible to call the person back on the same number.

This was one very important feature that made iOS 8 very useful. Apple has taken away a very important feature.
Seems like a bug introduced in IOS 9
To me this seems like a bug introduced in IOS 9 that should get fixed automatically in future.
For outgoing calls, it continues to highlight in blue the specific number among multiple numbers in the contact on pressing ⓘ in the recent contact list.
For missed calls, it has stopped highlighting in blue but it still continues to show the label (like iPhone, mobile etc. ) for the missed call number on the main screen having all recent calls.