Anna Davis, the 2022 Augusta National Women's Amateur champion, missed the cut by exactly one shot after receiving a one-stroke penalty over her pace of play.
The cut line after Thursday's second round was 3-over par.
Davis shot an opening-round 70 and would have made the cut on the number.
When the penalty stroke was assessed, it brought her second-round score to a 6-over 78.
"Anna Davis was assessed a one-stroke penalty for violation of the Tournament's Pace of Play Policy," rules committee chairman Jim Hyler said in a statement.
"Her group, which included Lottie Woad and Maria Jose Marin, was notified that they were out of position multiple times during their second round. While being timed, Davis received her first bad time after playing her second stroke on hole No 5 and received her second bad time following her second stroke on hole No 17. She was subsequently assessed a one-stroke penalty, which was applied on hole No 17."
Davis won the prestigious ANWA as a 16-year-old but was also involved in a rules controversy in 2023, when she was docked four total strokes for lifting and cleaning her ball when "lift, clean and place" rules weren't applicable to the conditions. She missed the cut by two shots.
Davis is a freshman at Auburn and achieved a personal-best ranking of No 4 in the World Amateur Golf Ranking.
Woad, a 20-year-old from England, held the lead after two rounds at 5-under 139. The first two rounds were played at Champions Retreat. The players who made the cut will play a practice round on Friday at Augusta National before contesting the final round there on Saturday.