I apologize for any inconvenience caused.
What you are telling us is very rare, and we have not been able to reproduce it.
With Bom Stock Control enabled, the calculated stock of the products that share BOM with the one in the order should be recalculated, according to the qty you have configured in each one.
Please, can you open a private ticket in order to investigate? There you will be able to provide us with your website credentials and we will take a look to see what is happening.
This is the link to open the ticket: https://stockmanagementlabs.ticksy.com/ticket/
Remember to make a reference to this post.