How to fix the overlay of a transparent texture on a basic texture?

[mild hedge]

!faq render-order

[agile coral]

(Result for "mc-render-order")
If you use semi-transparent textures (like colored glass) you need to move elements with that texture to the bottom of the element list. Otherwise elements behind these semi-transparent ones won't render ingame.
For the Bedrock Edition this also applies for cubes, but groups are rendered alphabetically rather than by their order in the Outliner (=bottom right section In Blockbench).

Disclaimer: Keep in mind that this won't necessarily change how Blockbench renders it, meaning it will most likely still look weird from certain angles. In rare cases the aformentioned steps also don't help ingame either for some reason.