I've seen that before.
Did you also leave the Sky Dragon (Hylea's quest) and the dragons of the White March alone, though?
I got called a dragonslayer too, even though I left the Sky Dragon alive and let the Adra Dragon take over Falenroed. However I did kill the Alpine Dragon. I'm just confused about how a pirate in the Deadfire knows about it, but I suppose it's possible.
It's a little weird, but I assume if anyone kills a dragon it'll end up being big news somehow. Game-wise it's just a simple check I guess if you ever had killed one of the three (5? if you count the Mowrghek ones from WM2).