Check that you are inserting the vias correctly so that they are inheriting the net names from the track which they are to be part of. See the Tutorial about how to do this.

How to avoid the problem that you have placed a via by hand and then not assigned the netname to it. You do not need to place vias by hand. Here's the correct way to insert vias: 1. Start the trace on your desired layer; 2. Left click once to end the track on that layer; 3. Press the letter or number key for the layer you want to swap the trace routing to (for example, if you started routing on the Bottom layer, when you press the **T** key routing will swap to the Top layer); 4. A via will appear; 5. Do not click anything: just continue routing on the new layer and end routing in the normal way adding more vias in the same way if required.