I don't know if anyone else has brought this up yet, but it happens a lot -
When I conquer another civ's planet I often get their Manufacturing or Technological or Economic capital with it, when I already have these on my colonized planets. The new duplicate versions can't be demolished! So it's a waste of a planetary tile essentially.
I don't know if this is a bug or intentional, but it'd be nice to be able to demolish them.