Reproduction steps:
0) Look at atached gif.
1) Open "Test" project, proceed to scene "Stage1"
2) Click play - everything works as expected. Exit play mode.
3) In hierarchy click on object "player" then in the animator window click on any animation transition and enter playmode.

Expected result: As in step 2, everything should work fine.
Actual result: Errors in the console due to missing reference.

NOTE: Scripts are unable to get reference to script on "player" object after sequence of actions mentioned in 3rd step.

Workaround: Don't click on the object containing animator that you are going to edit.

Reproduced with: 5.4.0b1, 5.3.1f1, 5.3.1pi, 5.3.0f4, 5.3.0b1;
Regression introduced in: 5.2.4f1.