A common problem with Civil 3D. If you have a surface with a hole, the hole will not be filled with the surface you are pasting into. It will triangular across the hole like below.

Pond with hole in middle

When pasted together the middle is wiped out. Rather than the middle been taken by the existing surface pasted in first.

I know you can create a “hole surface” as workaround, but this isn’t as dynamic.