From the sounds of it, you are using the not-included-dig-hole tunnels and the problem is caused by how the terrain works. In order to "punch" through the terrain, you need to use what is called a dig-hole. A dig-hole is basically an invisible mesh and has a marker thing on it in Surveyor for us to see that opens up the terrain so that tunnels can pass through the landscape without having the ground end up filling up the tunnel entrances.
There are two types of tunnels. Those that have the dig-hole attached to them along with the humungous tunnel entrances to fill in the space around them, and those that you have to put together yourself. The roll your own kind consist of tunnel wall splines, separate track and manually placeable tunnel entrances. Like all assets some are better than others in both categories.
Dig-holes have their own issues. They need to align with the grid, making them difficult to place, and this also affects how the tunnels will align on the terrain. Dig-holes can also open up more terrain than you need, or sometimes not quite clear enough because the tunnel falls on a sloped terrain at an angle instead of head-on the N-S-E-W alignment. The fix for this is to use splines and squish the terrain to cover over the space between the tunnel entrance roof and the land behind and around it. Sometimes though, you're lucky enough to have everything line up. When that happens, crack open your favorite drink and celebrate.
In all honesty, tunnels have always been an issue. Hopefully someday N3V will come up with a better solution to this age-old problem.
