Eunan O'Kane fired the Cherries into a first-half lead before Marc Pugh was booked for diving inside the box when the he was convinced he should have had a penalty for Roman Golobart's challenge.
Then Bournemouth were equally convinced Simon Francis had not fouled Maynor Figueroa for the Wigan penalty from which Gomez equalised, the midfielder tapping home the rebound after Shwan Jalan had saved his initial effort.
"Marc is not the type of player who goes to ground easily," said Howe of the first incident.
"If he goes to the floor I would bank on it being a penalty.
"And their penalty was disappointing. It was one of those 50-50 decisions and unfortunately it went against us."