Footage emerged of fans at both grounds igniting fireworks and aiming them at the players on the pitch.
Police were forced to intervene in both Essex and Ireland as supporters refused to stop when asked over the stadium tannoy.
Waterford's clash against Shamrock Rovers was suspended after the fireworks exploded onto the pitch. It's understood the fireworks were ignited from the away stand.
Players and staff were protecting their heads as they ducked for cover, however, Waterford's Anthony Wordsworth was visibly injured by the fireworks and received assistance from teammates after being struck twice.
Referee Rob Hennessy duly suspended the match, which restarted after an eight-minute stoppage. Shamrock Rovers went on to win 3-1.
But Hashtag Reserves' match against Concord Rangers was abandoned after fireworks were aimed at the pitch.
Hashtag player Matas Skrna fell to the ground after being struck by the firework. The club have since confirmed the player is okay.
A post on the club's Twitter account read: "We expect fireworks whenever @hashtagutd play but not like this!
"Our player, Matas Skrna, is luckily ok but this could have been bad!
"Game abandoned at 2-0 up as house where fireworks came from refused to stop. Two more landed near pitch. Police have been notified. Stay safe."