This looks like a bug related to the "sorting problem". It appears as if image empties are being alpha blended to the color buffer after all regular Alpha Blend objects, so they always appear on top.
You can switch the blending mode from "Alpha Blend" to "Alpha Hashed". This will give you a really noisy blend, but it gets the ...
I assume this is under Cycles.
Double-check that the Base Color is full white. By default, a "fresh" Principled Shader uses 80% linear white (i.e., all RGB channels=0.8, not 1.0). In addition, you'll want to change the IOR to 1.33, so the drops are water, not glass.
Beyond that, you can try replacing the Principled BSDF with a Refraction BSDF (also with ...
There is a trick that worked very well for me. You can make the object "invisible" inside of the clear sphere by adding another sphere just slightly smaller inside of it, adding a Boolean modifier to both the water inside the sphere, and itself. Then set the Boolean sphere to fully transparent so you do not see it. Now the water inside of the sphere will ...
You have to change the Blend Mode in the material settings and have to be in Rendered View.
Any of Alpha Clip, Alpha Hashed or Alpha Blend would work for a single image, but for a pixel perfect preview in EEVEE, Alpha Blend is required.
Use alpha blending to overlay the surface color on top of the previous color.
Welcome to Blender! It's a big, complicated piece of software where lots of things can go wrong, and it takes a lot of practice to get used to it, so no real surprise that you had a tough night working on this.
In the posted .blend file, the "inner crystal" had no material, so maybe you uploaded it before shading it green and blue.
The "outer clear part ...
You can use Light Path > Is Singular Ray to "mask" inside object out of main object.
Node setup below should be assigned only (!) to the object you want to hide. Sphere has simple Glass shader.
Another crucial thing here is Glass Roughness. You must add "something" (more then 0.017-0.18) not to break refraction. I've added 0.033.
There's still residual color information in the alpha area of your png. The better way to fix this is to get rid of the color mix node. Create a seperate shader for your screen-print ink material and wire that and your glass shader node into the mix shader node. Now drive the shader mix with your alpha channel.
This also allows you to modify the material ...