The bug

In general, Programmer Art does not duplicate texture files which would be identical to that of vanilla (as explained in MC-266281). However, there exists at least one counterexample with respect to item textures.

Affected texture files

The file leather_chestplate_overlay.png is completely visually empty in both the default textures and Programmer Art. However, in Programmer Art, it contains several pixels set to an alpha of 0, meaning that the file sizes are different.

In addition, the file melon_seeds.png is also different, however this was due to a bug (MC-200957), so it's probably not worth keeping this old, bugged version of the file around in Programmer Art.

How to fix

Delete these texture files from the Programmer Art resource pack.