Since the person who has an issue here is the new junior developer, complaining to upper management that someone "doesn't understand logic" seems like a terrible idea to me. Such an action could make this new junior employee look like he/she is the real problem here.

Depends on your organization. Sometimes it works, sometimes it backfires completely, as both levels of management get frustrated with you.

My favorite anecdote surrounding that is when a team member was highly frustrated, and send an email to our boss' boss (the CIO), explaining the frustration. The CIO forwarded it right back to our boss with a three word response: "Fix your employee."

I'm not saying he was the greatest CIO ever, but it does show that the results might not be what you expect or desire.

Almost never a good idea to leap the chain of command. It's universally hated and OP hasn't even gone to his own manager yet.

Sounds like an excellent idea. And probably bring several concrete examples of the issues.