I used Recruit Misfit ability of the Pirate Captain and even though the mana was spent, it did not recruit a random rouge from my deck. Has this ever happened to anyone?
I don’t actually recall this ever happening to me (except for the last case). It may have happened otherwise and I forgot it, though. 
So, do you have any screenshots? Can you tell us a bit about the surroundings and circumstances?
Maybe share the game link, if possible?
Have you refreshed the game? Or the whole browser?
Can other people see you didn’t get anything and there is a countdown on the relevant Pirate Captain
(if you are playing a multiplayer game)?
Is it listed in the Events tab?
Or, have you checked in your deck (not your hand!) and you do have one to deploy? Because if there isn’t any, it still activates the power, but gives nothing though.
It turns out that I did not have any rouges in my deck. I had a goblin, which was an archer, but that doesn’t count. I saw this by trying it again once the countdown was over. There’s a brief tooltip text that appears saying there are no cards. I also had some in my hand but that also does not count; it has to be the deck.
What is the “Events” tab?
Glad your issue got resolved! 
The Events tab is a very important place where you can see a history log of triggered abilities, Boss spawns, fall of settlements and more!
You can access it by opening the chat, and then at the top right there click on the Events tab. There is also a
- Diplomacy tab where you can send private messages.
- A Combat tab where you can see all the battles you have been a part of, even those involving allies!