The FA is believed to be seeking observations from Deeney after he accused Cherries midfielder Dan Gosling of 'trying to do' Tom Cleverley and for criticising referee David Coote.
Deeney scored twice and set up Ken Sema at the Vitality Stadium, while Bournemouth hit back through Nathan Ake, Callum Wilson and Ryan Fraser.
Watford's Abdoulaye Doucoure was lucky to avoid a red card for a tackle on Fraser, while Gosling was booked for a late challenge on Cleverley. Deeney told the BBC however that he felt referee Coote ducked out of some big calls, and now the FA has called on the striker to explain himself.
"Abdoulaye Doucoure probably did get lucky [not to be sent off], but you can't tell me that their boy did not try to do Tom Cleverley," said Deeney.
"They know it. We know. But the referee bottled it on a few occasions today."