Can you share the model? It’s probably too small, you can try scaling it up 100 times, if it doesn’t work I’d use curviloft. Since it’s a symmetrical shape you can model just 1/4 and the use either rotate and copy or mirror and copy.
I would go back and make the disc whole again (and be sure it is its own component).
Then use follow me to make the pipe shape (whole pipe, not half). This would be 1 ‘L’ shape.
I would then position my pipes to make the pattern I wanted and use the solid tools to union them together. Make sure the ends of the pipe stick past your disc.
Finally use solid tools to subtract the pipe cross shape from the disc.
Looking at your screen shot, I would guess you are running into the small face limitation issue. Scale the whole thing up by 100, try follow me again, then scale back down.