The intermittent flow of prisoners could affect your prison income temporarily. Arrivals and exits are designed to have a permanent workflow in your prison, but your cells don't need to be full at the same time to succeed. 
You don't have to worry if you spend some in-game hours with income losses, or with an empty module. This will change relatively quickly, and you will recover your income flow soon. All the prisoners' checkouts will provide enough money to balance your profit and loss account during these hard moments. 
If you are aware of this possibility, your strategy will be more efficient if you try to save some extra money in times of prosperity. 
The first bus in the morning will bring new prisoners if your prison spent the night with some vacant cells. This normally happens at higher points of progress.