Assuming that you're using two-cab DC control, then you would have switches to choose which power pack to control which block. If you wanted a train to move from one track to another via a double crossover, ideally you'd set the cab control so both blocks (the one the train is in) are under control of the same cab. If there were two trains in the same block or in different blocks under control of the same cab, they would both move when you applied power from the powerpack.
If you were using DCC, then no problems at all--the other train is addressed separately.