Unions causing my dome to look like it exploded

Hello! I’m trying to make a dome around a space station I’m designing, but when I negate a part to create the dome shape and union it, it’s fine. However, when I try to negate holes in it to form tunnels leading out of the dome, it looks like the top shattered or completely exploded, and I don’t know how to fix it. I need both a dome and the tunnels connected, but how would I do this without unions?

Here’s a photo of what it looks like before unioning in the parts to connect the tunnels

And here’s what it looks like afterwards. Is there any way to either fix the problem or make the same thing somewhere else?

The way the union system works is a little tricky, but my suggestion would be to make the holes for the tunnel and then do the glass shattering on the dome. Union negating typically goes in the order of part selection so if it doesn’t come out right the first time try switching the orientation of selection before negating.