Overlapping cells with Sites.Count of 2 or 3

[chomi3]

Hey

When I create diagram for small number of cells, like 2 or 3, the cells tend to overlapp.
The site coords is fine (both sites are in their respective - separated positions - visible on the screenshot as numbers), but the second site has the same vertices / edges as the first one.

I spend 2 days trying to debug it, and honestly have no clue how to deal with it.
Could you please point me in the right direction?

On the second screenshot you can see both sites manualy separated, to better visualise the issue:

Thanks