The antennas are not meant to be placed inside of your craft, but rather on the side/on top.
You cannot place anything on top of an antenna either. In your screenshot you seem to have placed your antennas on the bottom of your capsule or heat shield, making it impossible to (re)connect the rest of the rocket.
(In theory it is possible to place the antennas inside of a craft, using the offset option, but then you (probably) won't be able to deploy them because they are 'trapped' inside the craft)
