The resource pack attached to MC-212630 offers a complete fix for this issue. Mojang have my full permission to (and are encouraged to) replace the affected vanilla model files with the contents of the resource pack.

The bug

The pumpkin/melon stem model's planes stretch all the way to the corners of the block, unlike other cross-shaped models, which stop just short of the corners. This is best seen on cross-shaped blocks unaffected by random offsets.

Usually this is unnoticable outside of stem pixels being slightly more rectangular than other cross model pixels, however custom textures can make this discrepancy more obvious.

How to reproduce

1. Download and apply the attached resource pack
2. Place down a cobweb on the ground, preferably in an environment that makes block borders easy to seen
   1. Note how its two texture planes stop just shy of the corner of the block
3. Plant pumpkin seeds on farmland
   1. Note how, unlike the cobweb, its texture planes do in fact meet up with the block's corners

How to fix

The resource pack attached to MC-212630 fixes this issue completely, alongside fixing multiple other issues with the stem model.