I came across the first bug a few days ago, although I'm not sure whether it has its root in the Source Engine code itself as I've experienced a similar bug in an official Valve game as well. Anyways, I was playing as Captain and fought off an enemy archer with the help of another Captain. After having filled my special bar, I loaded it into the blunderbuss and shot at said archer, who was retreating through the small tunnel to the bridge area nearby the castle. In the very moment I shot it away the other captain released his parrot and the projectile of my gun and his parrot got stuck in each other in the air. They remained in that position until the other captain walked up to them, touching the projectile and thus causing it to explode.
The second bug occurred to me while playing as Sharpshooter. The rifle was loaded and as soon as I had filled my special bar, I lighted the gunpowder bag and threw it. However, after having activated the special, I held down M1 to fill up the charge bar. Now, having it send on its way, the rifle automatically released a shot. I was a little bit confused and thought that I might have had held M1 for too long. But then I noticed that there was still a projectile in it, meaning that the shot which got released automatically (and also did no damage as far as I noticed) was just a-nothing and I could still use it without having to reload it. Now, it would be a great idea if some sort of mechanism was implemented, requiring you to release M1 and then press it again in order to be able to shoot.