We have the same experience.
It can re-produce easily.
tap the webclip -> Safari -> launch FileMaker Go -> open the target file -> close the file
Just repeat these process several times.
You'll find that sometime no dialog but sometime confirmed at Safari to FileMaker Go.
Solution is to use FileMaker Go App Maker v1.0.3 to make mobileconfig files with Web Clips
DO NOT USE iPhone Config Utility