Hello Mateusz Domański,
Welcome to microsoft Q&A, thankyou for posting your query here.
Check if there is sufficient IP address space available in the subnet associated with your VMSS.If the subnet is running out of available IP addresses, the third VM would not be able to provision correctly.
Check if the configuration of your VMSS regarding fault domains and update domains could be affecting the provisioning.
Verify that the health probes are responding correctly. If a probe fails consistently, it might prevent scale-out operations.
Hope this helps you.