Steps to reproduce:
1. Create a new PCB
2. Select TopSilkLayer
3. Create a circle (C)
4. Create a circle more
5. Select 1st circle
6. Make it "locked" (Important!)
7. Change Center X and Center Y to 0;0
8. Hold CTRL button and select 2nd circle (both circles are now selected)
9. Try to use "Align Vertical Center" or "Align Horizontal Center" or any other alignment behaves strangely
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Electron
4.2.10
Windows
10
EasyEDA
6.4.31