https://www.transportfever.net…133520-1-jpg/&thumbnail=1
never build intersections that close like the two in the middle. Cars will try to keep intersections clear and the space between the intersections is too small for multiple cars, so only one at once will be able to cross the intersection. In your picture it looks like the cars are not waiting and blocking the intersetction, this happens if you change something with the road and will usually sort itself out after a while.
Removing the traffic lights can add a lot of capacity to intersections and should fix the intersection with the railroad crossing. Other than that you really shouldn't have at grade crossings between railways and such big roads. Roundabouts can help, too, since they make the trip longer and people will try to avoid it by taking other roads or public transport.