Ramset nails not flush with basement frame wall
If this is a base plate on the floor for a wall, you're fine as is and it pretty much happens to everyone. The nail is embedded in concrete, the floor keeps the base plate from moving lower, the nail's job is to keep it from moving side to side, and the wall you build on top of it is what will keep it from lifting up the small distance you see there. I wouldn't attempt to force it lower since you risk bending or breaking the nail, or fracturing the concrete that you have a solid bond to now.

As for why this happens, not all concrete is the same strength, especially if it's had a long time to fully cure. A charge that might work on one floor can easily come up short on another. I've also seen a firm grip on the tool and solid hand with the hammer (for the hammer style ramsets) can make a big difference.