Thanks for sharing the data. I'm at a loss to explain what is happening, I can see the behaviour you are referring to. I did save the layer out to a new GeoPackage layer and the issue does not occur in the new layer. The issue on the gpkg you provided might be related to how it was created or something that has happened to it in the meantime.

I noticed that you said you copied the layer styles to replicate the problem. Can you confirm that there isn't a scale level set in the style which may be making points of a certain type not be visible? Also is there any chance of making the geopackage and style available for testing?

Can you amend your question to contain that detail. It may help people recognize the problem if they have encountered it before and subsequently provide you with a solution.

I know this was asked a while ago but I just ran into the same problem trying to make a vrt out of 1300+ files. There must be a character limit or some kind of limitation in the "Build Virtual Raster (Catalog)" tool. Because when I copy the text from the GDAL code box at the bottom of the tool and paste it in the command line my text stops midway through the reference to file 1076 (out of 1300). So as @radouxju suggests if you edit the command and execute via the command prompt you might have better luck - It solved my error.