I've noticed two bugs with omnis' flights:
1. When selecting an omni by its destination, I am unable to deselect using space, ESC, or by clicking the button. In order to deselect I have to select somewhere on the map.
2. If a game is loaded when an omni is in flight, I am able to move other omni's into its destination, allowing stacked omnis.
EDIT: I found another bug, double clicking with an omni on invalid terrain (on differing elevations) will select nearby ships, the same bug does not occur when attempting to build ships on invalid terrain, but the same thing occurs for both when building on valid terrain.
You are able to build omnis on omni destinations as well.
EDIT: Also done when a save file was loaded.