Playing as the Nakalim, I unlocked the Carrier class ship and started editing its default ("Chancellor") design. I tried to upgrade one specific pre-existing armor module, and found I couldn't do so. Take a look at this:

This is the ship's default design. You can see a projectile defense module in the centre.

When I try and insert a defense module in that same slot, it won't let me.

If I remove that original defense module, you can see it was magically inserted in a support slot! This is not just a visual bug either, as you can see the ship's defense numbers change when that misbehaving module is removed.