This has happened to me on Dersu Island.
The explanation is simple: mobs don't move while you aren't on the map. You can check this easily: lure a mob to the dock, leave the island, do whatever business you need on another place and then come back. The mob will be exactly where you left it before leaving.
Unfortunately, I haven't found a solution for this, you need to get stronger and beat the enemy. Maybe editing the savegame would allow you to change the locations of a given hero, I don't know.
Hope that for future patches/games the devs address this.
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