After a lucky David Morley own goal secured the points for Pools, the match was marred by the late incident at Victoria Park.
An FA spokesman had the following to say: "The referee mentioned in his report an incident concerning supporters entering the field of play and confronting a Macclesfield player. We have written to Hartlepool to ask for an explanation and they have seven days to respond. We have also contacted the local police and will be trying to ascertain how the situation was dealt with and what the club will be doing to prevent such an incident taking place in the future."