Afterwards West Ham manager David Moyes called for the fans to get behind the team.
Weak throughout the spine of the team, West Ham's cause was not helped in the 27th minute when Winston Reid was stretchered from the pitch with a knee injury that has since ruled him out of the rest of this season.
"West Ham United have immediately launched a full and thorough investigation into the incidents which marred the second half of today's match and are committed to taking decisive and appropriate action", it said.
"There is no place at any level of the game for what happened at the London stadium. There will be no further comment at this time".
West Ham's James Collins was confronted by protesting pitch invaders in the defeat to Burnley.
He said he hopes the fans got their anger off their chest for future home matches, and admitted playing is a struggle right now.
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"We had played well enough to be in front but the first goal quickly altered things".
Moyes spoke about the moment Mark Noble clashed with a pitch invader and admitted that he thought the Hammers skipper might have been sent-off for his actions: "A little bit (though he might be sent-off)".
"We have got nine finals, that is the reality", the 33-year-old Argentine said in an interview the official club website. "But for the time I've been here, I've certainly enjoyed it". For the majority of the time I've been here, I think the team have done a really good job. We needed the supporters with us in a different way.
"I've told them (the players) that we're all sticking together, that we're going to stick our chests out, get back to winning ways and do it together".
"We need to play better for longer periods, and defend better in the short periods we're put under pressure". I think we've got attacking players that can score, they didn't score today. However, both players are too inconsistent and will find life tough against one of the hardest working teams in the league.
"We scored a top goal, a great pass from Matt Lowton and a fine lay-off [by Wood]".
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