Steps to reproduce:

1. Open attached project "778046.zip"
2. Open scene "repro"
3. In hierarchy, select Cube and open animation window
4. Press record and in inspector change y value of Cube's position
5. Notice that Transform position property is added to animation window
6. Expand that property and remove keys for x and z values
7. Go to another keyframe by clicking on Timeline in animator window
8. Stop recording
9. Notice that x and z position properties are set to 0

Reproduced with: 5.1.4f1, 5.2.4f1, 5.3.4f1, 5.4.0b10