Did you capture the planet after you bombed it out?  In that case, the enemy structures continue doing what they do (but they can't build ships).

Or did you capture the structure with that new capital ship?  Can you even do that?  I thought it only worked on frigates.

I've had this happen to me, I captured a pair of frigate factories, and they continued producing enemy ships. I was unable to control them in any way aside from scuttling them.

Captured Gauss Guns were also a little wonky, I think I saw them auto-firing at eachother, unlike the frigate factories though, I could control them and direct their fire.

Yes they where captured with the new capitol ship (I can't remember the name at this time )

The exact order of battle was:

1. Enemy owned the planet, (with a broadcast center in orbit)
2. I attacked, took over the broadcast center (with the new capitol ship via boarding)
3. I bombarded the planet to extinction
-I then waited a long time (waiting for the future to dissipate, it didn't, and I can confirm that there was no other enemy broadcast centers in the system/surrounding system. )
4. When I scuttled the broadcast center, enemy culture started to subside (and my culture began to pour in from surrounding areas).
5. I could then colonise the planet

Results:

-My culture from other planets started to close with the planet. (I suspect this is because of a reduced culture block rate from destroyed enemy capitol ships/planet?)
-Enemy culture was still coming out of the planet
-Planet could not be colonised as enemy culture was too strong
-As above posts have stated, I can still scuttle the structure