If you are seeing an orange dot on the center of the Main Menu button this is an indication that either your Pokémon storage or Item Bag is full. Tap on the Main Menu button to see an indicator of which inventory has reached its max capacity.
Transfer Pokémon to Professor Willow to free up space in your Pokémon storage. Use or discard items to free up space in your Item Bag. Additionally, you can increase either Pokémon storage or your Item Bag by purchasing an upgrade in the Shop.