Hello, even after I destroy the enemy bases that pop up, I cant target the nuke silos to destroy them and they still fire on my base even 10 minutes after i destroyed the enemy base with the nuke silo. Is there something special you need to do to destroy them?

Based on the information you provided, I cannot determine the cause. May I ask which map you are playing in?

In some worlds, fortresses spawn in sets of three. In these cases, you must destroy all enemy fortresses before you can deal damage to the nuclear missile silo.

On standard maps, fortresses spawn one by one. After 8 fortresses have been generated, the biters will begin constructing the nuclear missile silo. To destroy the silo, you must completely eliminate the fortress that houses it. (However, sometimes the visual model of the silo can obscure parts of the fortress structure. Therefore, you might think you have destroyed the fortress when you actually haven't. Please rely on the in-game text prompts for confirmation.)

It was the Valley map, we destroyed everything in the base and the walls fell down but we couldn't destroy the silo.