I've encountered this too, in the end I simply disbanded the unit and placed a different merchant ship to take over. Haven't seen it since, with ships at least.

Currently my full stack of line infantry, trained to destroy the pirates in antigua, is stuck on one of those little islands with an arrow pointing to their capital island. The stack won't move and won't board, it keeps on telling me it just wants to hang out there. In the meantime, the stack of pirates on their main island is getting bigger and bigger. Waste of a beautiful surprise attack if you ask me.

And I'm playing the UP, on Hard/Hard. Version should be the latest there is.