Here are the steps, it happens randomly

1. Build a Nether Portal

2. Go into the Nether Portal

3. Sometimes when you leave that Portal from the Nether back to your overworld, either you'll teleport near the primary portal that you went into, and sometimes when you leave the Nether, the Nether Portal in the overworld could spawn you 1000s of blocks (meters) away from your base, which makes it extremely annoying to head back to the base while it is 1000s of blocks away!