The easiest way to fix this is to draw an entrance without the actual door being shut.
When exiting a normal door, the overlay of the door appears, which means, your door appears on the exact X and Y of your house. Walk around the village and the opened door should be glitched somewhere.
You fix this by openin the entrance in HM and going into Exit properties. Then select wooden door and fix the X and Y to a new number depending on which quadrant the door is in, when you press the Grid on overworld. If X quadrant is 25, multiply this by 2= 50. Same for Y. This will get the door overlay close to your location (but not fully). Then make a final correction: bigger X is moving the door right, bigger Y down, until the overlay is centered right above the door.
Easier solution: select the door= none, and place the white exit dot lower (Link will not walk over the door this way).