Two very simple cases are presented here, but I assume there are more. Both scenarios require the player to be the leader of a group of a bunch of more units. That's it.

Case 1: doStop and doFollow

1. doStop all units by script.
2. Try to make the follow you again (1-1 Return to formation). They wont.
3. make all units doFollow player by script again. They will.

Clearly, direct commanding should take uttmost priority, or a script that doStops a unit of the player's group will be essentially deadlocked.

Case 2: setUnitPos

1. setUnitPos your units to "DOWN".
2. Try to make them go back to normal with direct commanding (7-9 Automatic stance). They will stay down and comfy. You can force them to "UP", but upon issueing 7-9 again, they're back to the scripted thing, which is wrong.
3. Issue all units to setUnitPos "AUTO" by script. Notice how things are back to normal/responsive again.

7-9 is the direct commanding equivalent to setUnitPos "AUTO" (althought it comes with a "funny" description). It doesn't work any more with a script taking precedence, which is clearly wrong.

A simple setup as follows (and with a group and the player as leader) will do for a reproduction mission:

THE_GROUP = group player;
THE_LEADER = leader THE_GROUP;
THE_UNITS = units THE_GROUP;

DO_STOP = {
	{
		doStop _x;
	} forEach THE_UNITS;
};

DO_FOLLOW = {
	{
		_x doFollow THE_LEADER;
	} forEach THE_UNITS;
};

DO_DOWN = {
	{
		_x setUnitPos "DOWN";
	} forEach THE_UNITS;
};

DO_AUTO = {
	{
		_x setUnitPos "AUTO";
	} forEach THE_UNITS;
};