As far as i can tel there is no way to prevent this so it is going to be treated as a bug.

When you place your power armor in Sanctuary, Even in a repair dock it will have it's parts stolen by your own settlers i have to assume since there are 2 turrets by the armor station and they are still operational.

I have tried removing the fusion core but it didn't help at all the parts on the frame still disappear.

This seriously needs to be patched as you can't just get new power armor parts anywhere you want. If settlers use your stuff and it gets destroyed then it should be sent back to your workstation so you can repair it or to the inventory of the settler that took it. option 1 preferred of course. Also have a settlement log so if things happen like this when you are away your settlers tell you what has happened.

Are you using any mods?

The settlers aren't taking your components. They'll take a full suit if it has a core in it, but not the pieces off of the frame. If the pieces are disappearing, than it's a glitch. I've never experienced this specifically, but it sounds similar to the Cell Reset Bug that occurs with mods that make edits to map cells.