Clean up feature applied on canvas with benzene ring and stand alone molecule moves it (s/a molecule) to the top left corner

**Environment details (please complete the following information):**
- Indigo Toolkit Version 1.18.0-dev.2.0-g369c82f8c-x86_64-linux-gnu-11.4.0
- Ketcher Version 2.17.0-rc.2 Build at 2024-01-03; 17:17:22
- Chrome Version 120.0.6099.130 (Official Build) (64-bit)
- Win10
- Issue found while testing https://github.com/epam/Indigo/issues/1440

**Describe the bug**
Clean up feature applied on canvas with benzene and stand alone molecule moves it (s-a molecule) to the top left corner

**Steps to Reproduce**
1. Load from file: [ChaoticLayout.zip](https://github.com/epam/Indigo/files/13872909/ChaoticLayout.zip) (unzip first)
2. Press Clean up button (Ctrl+L)

**Actual behavior**
System moves stand alone molecule to top left corner

https://github.com/epam/Indigo/assets/26869421/998bcfe0-fc7c-4150-b1f6-d909db95a9a7

**Expected behavior**
Stand alone molecule remain in place (more or less)