Dear tengtongseu, without seeing your model (not even knowing if you are creating it in ATENA Science / GiD or ATENA Engineering 3D) and a sketch of what you are modelling, it is hard to guess what can be the problem...
For modelling construction process, please understand the following:
1. the newly added elements have to be SLAVE in the connection
2. the connected nodes are shifted according to the current position of the already existing part of the structure. Please note only the nodes in contact are being shifted, i.e., if the flange is wider that the web, only the nodes above the web are shifted and the rest are placed at the unshifted positions.
3. as long as only one of the macroelements/volumes connected by a an interface exist, the interface settings do not have any influence as no elements exist for the interface
4. numerically modelled contacts have finite stiffness. If the deformations are scaled up largely, it is normal to see some overlaps.