I'm all-too-familiar with this bug, especially since 99% of my builds are symmetrical (even the one build that isn't mirror-symmetric is radially-symmetric instead).
The bug can also present itself in other forms as well: Any sign of the grid shifting, no matter how slight, is a sign that this bug is surfacing. Side effects include the inability to place zooids in areas that you usually could on the other mirrored half of a symmetrical siphonophore (i.e. the game is literally forcing asymmetry), and sudden distortion while placing zooids.