Flooding
If the underground tunnel is below the natural water table, there will inevitably be seepage and eventual flooding of the tunnel unless a waterproof barrier is used to seal the tunnel from the elements. The challenge is that this process is very expensive and time consuming. Even one small compromise of that barrier can lead to flooding.
Gases
Tunnels don't always contain breathable oxygen, or may have a mix of oxygen with other toxic fumes. Asphyxiation can occur if there is a build-up of dangerous gases such as methane, carbon dioxide, carbon monoxide and blast fumes from the explosives used to create the tunnel.
Collapse
The famous 2010 mine collapse in Chile is just one reminder of what challenges tunnels present. In the United States alone, an average of 50 to 60 miners die from tunnel, cave and mining accidents every year. Tunnels need to be fortified to prevent ceiling collapse due to seismic activity or unstable mineral composition.
Temperature Extremes
Aside from ice tunnels, which can cause hypothermia, people often mistake tunnels to have a constant of 50 to 62 degrees Fahrenheit since they are underground, but there can also be extremely high levels of humidity and heat if they are located near geothermic activity. The "Giant Crystal Cave" in Mexico's Naica Mountain has a constant temperature of 120 degrees Fahrenheit.
Animals
Bats present a challenge for tunnels in that their droppings, known as guano, fall to the floor of the tunnel and decompose, releasing dangerous levels of methane over time. Aside from bats, snakes and spiders can be hard to get rid of if the tunnel is going to be used by humans on a regular basis.