I was noticing this, so I went and tested my theory.
Tiles that have multiple improvements will always be pillaged/bombarded in a specific order: Rails; Roads and Improvements; Fortresses.
If a tile has, say, a road, irrigation, and a fortress, the first successful bombardment/pillage will destroy the road and irrigation, but leave the bunker. The next successful strike takes out the fortress. If that tile also had railroad in it, then the first strike would only take down the railroad improvement, with two follow-up strikes necessary to take out the rest.
I have yet to see how this works with colonies.
Tiles that have multiple improvements will always be pillaged/bombarded in a specific order: Rails; Roads and Improvements; Fortresses.
If a tile has, say, a road, irrigation, and a fortress, the first successful bombardment/pillage will destroy the road and irrigation, but leave the bunker. The next successful strike takes out the fortress. If that tile also had railroad in it, then the first strike would only take down the railroad improvement, with two follow-up strikes necessary to take out the rest.
I have yet to see how this works with colonies.