I have read that he shouted, "The Regulars are coming", meaning the Regular Army.
It is important to realize that the citizens of the Boston area were opposing their own army which was directed by the lawful government of the day.
That government was a tyrannical monarchy which was fully supported by about a third of the population and tolerated by an additional third. The militia which surrounded Boston and eventually forced the retreat of the government fleet there was acting entirely outside government sanction. Even the Declaration of Independence was still over a year away.
. . . nor had men like John Adams even broached the subject of independence from England, if I remember correctly. The colonials were pretty much merely attempting to reinforce their rights as Englishmen.