Sometimes, if you attempt to select a region and fill it in the sandbox, some pieces will be left out, and they are the spaces that were locked last time you were in game mode. Steps to reproduce:
Load sybypom (for example). Note how the pipes are shaded blue, but the yellow/black tiles are not.
Enter sandbox mode
Select a copier (for example) from the toolbox.
Select the whole thing using shift+click.
Press F
Notice that the squares that were shaded blue in game mode (the pipes) do not change.