I've found two bugs that bug me;
1) It is possible to fit a 1x1 plate into a hole of a Lego technic brick, but not a 1x2 or longer plate. In real life though, this should very much be possible.
2) From experience I know it is possible to put a 1x1 round brick onto a peg, doesn't matter what the peg is attached to. However, in LDD it is not possible, only the really short sides of a peg and the axle with a stub on it;