Reproduction steps:
1. Open project attached (PartialClassBuild.zip).
2. Build it on standalone player.

Expected result: It will be built successfully.
Actual result: Building stops, output from console: (NOT ALWAYS!)
Error: "Type '[Assembly-CSharp]Player' has an extra field 'FieldTwo' of type 'System.Int32' in the player and thus can't be serialized (expected 'FieldOne' of type 'System.Int32')"
Error: Type '[Assembly-CSharp]Player' has an extra field 'FieldThree' of type 'System.Int32' in the player and thus can't be serialized (expected 'FieldOne' of type 'System.Int32')
Error: "Fields serialized in Editor, class 'Player'
'FieldOne' of type 'System.Int32'
'FieldTwo' of type 'System.Int32'
'FieldThree' of type 'System.Int32'"
Error: "Fields serialized in target platform, class 'Player'
'FieldTwo' of type 'System.Int32'
'FieldThree' of type 'System.Int32'
'FieldOne' of type 'System.Int32"
Error: "Error building player because script class layout is incompatible between the editor and the player."

Note: This does not appear all the time. If it is not reproducible from first time, just makes some changes (add space) in Player.cs.

Reproduced on: 2017.1.0a3, 2017.1.0b1.
Works fine on: 5.6.0p1.
Regression introduced in 2017.