When I wanted to mine my boat at the back( behind the last cat), In place of mining my boat, I was mining the block below the boat.
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I am unable to reproduce this issue. I am still able to destroy the boat around the back end of it whilst two cats are in it.

I think that the problem just was that a boats hitbox doesn't change when the boat is turned
If this appears to be your problem, then this report is a duplicate of MC-91376, which was later resolved as, "Works As Intended". This problem that you are experiencing isn't actually an issue and works how the developers intended it to.
Hi!
So you'll do f3+b to shown the hitbox and hit the bigger one
Hope it help's you.