The incident at Millwall came just over a fortnight after it emerged that the Football Association of Ireland was investigating whether Swansea forward Adam Idah was racially abused by Israel supporters during a Nations League fixture with the Republic of Ireland last month.
Matos has spoken to Idah, 25, about what occurred during a match played in Serbia.
“It’s a different situation because in the end the referee [in that game] said he didn’t hear anything so they could not stop the game,” Matos said.
“I was not there, so it’s hard for me to judge the situation.
“I was there [at Millwall], I was quite clear the fourth [official] followed the protocol, which I think is the right thing to do in these situations, and now there’s an investigation.”
Eom, an unused substitute at Millwall, has been in fine form for Swansea this season, while he also helped South Korea win the Asian Games earlier this month.
He will be in contention to feature when Swansea, who are top of the Championship, host third-placed West Ham United on Saturday (15:00 BST).