Is this a super small frame? Usually the down tube and top tube never meet.

Photos would help, although these kinds of alignment issues are hard to photograph.

You bought an old-stock bike 4 months ago. DId you buy it from a local bike shop, or over the internet?

If the bike rides fine, I'd probably ignore it. It sounds like it is unlikely to be an issue that will cause any problems, and there isn't an easy fix.