The cargo containers weren't intended
to come from the Botany Bay
, as they were painted with UFP and Starfleet symbols and shaped like the Starfleet containers seen in the previous movie.
However, the actual movie shots don't exactly reveal the UFP symbols on the outer surfaces, or the fact that the containers are attached to a workbee frame. All we see (vaguely at that) is that they are shaped like the Starfleet containers, and that they have Starfleet symbology on the inside. But that symbology is just writing on the wall, and those particular pieces of interior wall might have been patches installed by Khan using Starfleet materials. So perhaps there's some room for argument there.