When creating a custom Itemmodel for bottles (both splash and drinkable) they don't get colored automatically in the right potion color. Also there is no way to color them manually, so all bottles got the same color.
I attached a screenshot of my testmodel to this report.
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Where would you add "tintindex"? Because I've tried adding it and it doesn't work and I'm not sure if I added it in the wrong place.
See the German Wiki for the block model format: http://minecraft-de.gamepedia.com/Mcmeta_Format#Block-Modelle
Perhaps try adding "tintindex": 0