The club's involvement in the breakaway European Super League, which swiftly collapsed, had reignited lingering resentment of the ownership at Old Trafford.
The Glazers, who acquired the club through a leveraged buyout in 2005, have long been unpopular but became the subject of increased criticism in recent weeks.
Fans surrounded The Lowry Hotel, where United stay before home matches, on Sunday, letting off red smoke bombs and leading anti-Glazer chants.
The demonstration did not end there, however, with some supporters gaining access to the stadium and then the pitch, with flares hurled towards the directors' box and press area.
A minority of United fans clashed with police officers outside the ground, and Solskjaer feels that – coupled with the trespassing at Old Trafford – meant some took their actions too far.
"It was a difficult day for us," Solskjaer said ahead of Thursday's Europa League semi-final second leg against Roma.