Shape keys

Try to treangulate the mesh before export.

So your blend file is in gray…with a plane with some circular and square holes. Triangulating will help a little but its more than likely your topology and modifiers that are assigned to the plane.

It appears there are not enough vertices in your object to support the geometry you are trying to create. Could you provide an image of the wireframe with and without any modifiers you have applied to it?

My guess is there are just not enough edge loops/vertices to hold the holes in place and they are getting recalculated and filling those holes.

If you want could you share the blend file?
What version of Blender and Verge are you using?

So I have done many shape key models but none with holes like this.

Holes present a unique challenge. If the holes are within a defined region such that there vertex IDs are not re-ordered then the shape key will work. Otherwise what happens is the model itself distorts causing triangles to form and cross over other holes.

You can test this out by starting with a cube that has multiple edge loops or creating a simple subdivided surface so you get a grid across your base mesh. Then create your holes via boolean modifier or by hand.

Once you have these…move the hole around by copying its vertices only and you will see that the hole can not go beyond the next edge loop without those adjacent faces intruding into the hole. In effect filling the hole.

With the model you created you did not have any edge loops it was a single flat face….but in reality blender exports the face as triangles to make it GlTF compliant. The circular holes create a lot of faces equal to the number of edges.

With a single hole (circle or square or any shape) confined between edge loops there is no issue. But as soon as you have multiple holes and the shape keys require the holes cross edge loops the shape key will break. Not in blender because blender will recalculate the faces on the fly. GLTF however does not adjust the triangles or account for you moving an object outside its confined edge loops.

So…how do you create the effects you are trying to create.

I would divide up the object into smaller pieces. Left, Right and Middle section etc. Best if you could have one per hole. This way you can adjust the length and width as needed and the holes are confined to their own shapes and the shape keys will not have to cross boundaries.

After experimenting with this surface, I thought it might just be better to have an animated texture and a simple plane surface, but this approach may not work best for your needs.

Good luck this is a tricky one.

In the event you are really stuck having to use this sort of shape key and the shape keys distort there is a plugin called Transfer Vertex Order. That you can find for a few bucks and it will renumber all the vertices in your shape keys so they align if and only if you are not crossing boundaries.

All models will be triangulated on export to the engine, so better to do it manually to get expected result.