The Gunners ran out comfortable 3-0 winners at the League One club thanks to Mohamed Elneny's header and Eddie Nketiah's brace.
The betting patterns centre around the booking of Oxford defender Ciaron Brown.
The 24-year-old was shown a yellow card in the 59th minute following a foul on Nketiah. It was the only booking in the match.
The FA is understood to be aware of the matter and will investigate.
An Oxford statement read: "Oxford United can confirm that they have been made aware of a specific allegation of irregular betting around our Emirates FA Cup game against Arsenal on Monday evening.
"The club will co-operate fully with any investigation and while this is ongoing, we are unable to make any further comment."
READ MORE: Joao Felix excited to show what he can do in the Premier League after completing Chelsea loan move