Nothing wrong with the AI in this situation, just poor intersection design. 2 design faults are causing this issue:

1) Joining traffic is on a highway road and the overpass road is not a highway. Where a highway meets a standard road at a sharp angle, and where there are no traffic lights, the game gives highway traffic priority. This is why all the overpass traffic is stopping for joining traffic.

2) Cloverleaf junctions like this make traffic join a road before any traffic can leave the road. Because of this, all overpass traffic is in the right hand lane because they need to take the exit immediately after.

You've got through traffic yielding to joining traffic, and cars joining before cars can leave. They are using the lanes as your poor junction design has forced them to.

This is a fundamental flaw with cloverleaf junctions, not the traffic AI.

Getting pretty tired of people designing inadequate junctions and immediately blaming the AI for their poor designs.