You cannot specify ports in a DNS A or AAAA record. www.example.com cannot resolve to 1.2.3.4:443 and app.domain.com cannot resolve to 1.2.3.4:5555
If the application (be it a game or whatnot) supports it, SRV records can identify a port for a hostname. So, you could have minecraft1.domain.com and an SRV record to specify port 25565, and minecraft2.domain.com SRV 25566.
This means you can have multiple Minecraft servers with the same IP address, but you won’t need to give people the port numbers to remember; the hostname allows the game to look up the port via the SRV record.
This is great for selfhosters because we generally only get one IP (until they rollout IPv6; probably half the reason they don’t)
You can run into this issue with any two sync programs that operate on virtual files, as another commenter said. This isn’t specifically a OneDrive or NextCloud problem. You can safely run both at the same time on the same machine, as long as they are syncing entirely separate directories.
That being said, this is obscure enough that I feel like there should be some kind of check in these clients to make sure they’re not about to interfere with each other - users aren’t gonna know to check for this, especially since these clients are hiding what they’re actually doing behind the scenes!