Electrical – Duplicate Component Deisgnator

I am learning Altium Designer and therefore I've shosen simple audio project. For the sake of Multichannel Designm I've created simple audio input port, which I am multiplying with Repeat command and here is root sheet:

As you can see, AUDIO_INPUT is multiplied 8 times using Repeat command and here is AUDIO_INPUT "zoomed":

Now, when I try to compile the project, I get following error(s):

Class   Document    Source  Message Time    Date    No.

[Error] Sheet4.SchDoc   Compiler    Duplicate Component Designators J2 at 2950mil,5050mil and 2950mil,5050mil   20:05:54    16.05.2018  1
Class   Document    Source  Message Time    Date    No.

[Error] Sheet4.SchDoc   Compiler    Duplicate Component Designators J3 at 2950mil,4050mil and 2950mil,4050mil   20:05:54    16.05.2018  2

What did I do wrong? I tried to reannotate designators, I get same error.
Nomenclature:

1. Sheet4.SchDoc is root sheet
2. Sheet2.SchDoc is audio input sheet

I have deleted from and placed problematic components back to schematic and now the errors(s) are gone. But can someone tell me why?

ADDENDUM:
I have forgot to tell my project is under version control and I've commited project to repository, then deleted the contents of .Annotation file (I've left the EMPTY file itself in project structure) and it compiled ok, but I hardly beleive this is the right way to fix this problem.