Some features disappeared when using pbf

**mapbox-gl-js version**: Any version

**browser**:

### Steps to Trigger Behavior

Using PBF files, one of the point feature has a latitude of 0.000012. This point is displayed only when the zoom is greater than 12. If the zoom is less than 12, the point cannot be viewed on the map.

The test result shows that this problem occurs when the latitude is in the range of (0, 0.02).



### Link to Demonstration

https://jsbin.com/

### Expected Behavior

### Actual Behavior

Start by reproducing the issue with a PBF point whose latitude is between 0 and 0.02, especially 0.000012, while varying the map zoom around 12. Done means the point remains visible below zoom 12 and the behavior is covered by a regression test; the issue does not name a file or existing test to begin with.

Written by the indexing model from the issue text.