It's an issue with StreetComplete.  The freeway needs to be divided so that there are just small sections under the overpass.  It's a limitation of the databse and requires additional steps by the users.

I have been breaking up underpasses for this very reason when making edits in the area.

It shows up on StreetComplete if there is a bridge over the way at some point along the entire length.

I'm hoping this makes sense and helps.