One of the fasteners for the hood came off, and fell down by the stick, out of sight. Now, shifting from First to Second makes a noise and doesn't feel right.
All of the fasteners for the hood are required as the mounting locations serve important roles in the event of a collision. While shifting gears, the weight transfer and flex of the vehicle may be causing this noise through a now loose mounting location. Have a mechanic, like the ones here at YourMechanic, determine the source and cause of your shifting issue, and correct the situation.