Don't know about your door as to what kind it is. My metal door has a pretty thick and expandable rubber strip on the bottom. The downward pressure can be adjusted to fit down tighter or looser. When you make it fit down tighter then it conforms to any spot that would be lower or higher than the rest of the floor.
Mine is a Horman. You might explore it to see if yours could operate that way.
If your door is wooden then you can loosen up insulation strip and furr it to match the floor. Then reattach it.
You could grind down the high spot on the floor where the door lands or if it has the expandable rubber strip at the bottom, you can replace it with a thicker one that will take up deeper surface irregularities (may have to stop by your local overhead door shop to get it).
How much of a gap are we talking about?