Suassemblies break Save File

When I try to make a subassemby, sometimes I cant drag them out at all, but sometimes when it does work, weird stuff happens... When it spawns in, it can only spawn in the position in image one. then when I remove it from that position, for some reason the "ground" of the builder doesnt agnolage it, even if I set the comand chip as primary. Then If i load exit to the menu it just shows the default rocket, and then when I load it in it says it cannot load it in, and replaces it with the default rocket. same thing happens if i try and fly it. also the astronaughts stick their legs out, dunno if that helps