That should not cause any problems from the Active Directory side of things, as the two domains will essentially be like ships in the night - they don't know or care about each other. What you will want to do is be careful about how you design your DNS infrastructure.
Consider whether you'll need to resolve names in the subdomain from a system that's using the "parent" domain's DCs for DNS, or the reverse - you might need creative delegation (
NS records in the parent domain), forwarding (the subdomain's DCs using the parent DCs as their forwarder for recursive requests), or stub zones to account for the name resolution gap between your two Active Directory infrastructures.
Also consider that the search suffix of the systems in the subdomain by default would cause them to also search the parent domain's DNS for a hostname - this may cause some interesting and unintended problems.