Late in the second half of the Reds' 1-0 defeat a fan ran onto the pitch at St Helens' Langtree Park stadium and appeared to direct abuse at Liverpool striker Adam Morgan before tussling with stewards as he was led away.
There were also two instances of flares being set off in the stands, with one being thrown onto the pitch.
The Football Association have confirmed that they are looking into events at the match and are to write to the two clubs involved.
There were also reports of distasteful chants being made by a section of the visiting support but Merseyside Police said no complaints had been made to them and there was no record of any incidents in which they were involved at the fixture.
Fans of the two north-west clubs have a well-documented rivalry at first-team level but this is not the first time a youth team match has been affected.
Almost two years ago at an FA Youth Cup game at Anfield a minority of away supporters sang songs about the Hillsborough and Heysel disasters, a flare was let off, there were three arrests for drunkenness and six United fans were ejected from the ground.
