Reproduction steps:
1) Create a new project
2) Add an object to the scene (doesn't matter if it is an empty one or not)
3) Add any type of collider (2D also has this issue)
4) Try to edit collider ("Edit Collider" button in inspector window)
-- Notice that there's no handles which were used to modify collider's boundaries.

Regression introduced in 5.4.0f1