I happen to have the same issue on multiple saves. It seems to happen mostly when you connect a corner or central base section to the raft. It won’t affect pieces that only have one base attached to them, though. Just the pieces that have 2 or more bases connected to them.
I think this issue is caused by how the game is reading the positions of adjacent bases when determining if the piece is crucial to the raft structure when attempting to remove the targeted base. It’s likely missing a code to determine where the attached bases are in relation to the base you’re wanting to break down, as the game seems to be treating it as though the target is a central piece instead of a corner in most cases.
Hopefully this thought helps you guys find a fix for the raft base situation. I wasn’t sure where the main thread was for this issue, so I posted my reply here instead in hopes that you would see it.