Wrong stereochemistry warnings in 'Save Structure' and 'Check Structure ' windows

Affected version: Standalone

Steps to reproduce:
1. Execute /v2/indigo/check with the following parameters:
struct
[radium.zip](https://github.com/epam/Indigo/files/6278689/radium.zip)
options: {smart-layout: true, ignore-stereochemistry-errors: true, mass-skip-error-on-pseudoatoms: false,…}

Expected result: There are no stereochemistry warnings in both windows.
Actual result: A warning "Structure contains stereocenters defined by 3D coordinates,(0)" is shown in both windows.