We are aware of this problem and very sorry that it still persists. You can find an explanation for this problem from one of our developers, mowren, here: steamcommunity.com/app/268540/discussions/0/558755529550485100/
Unfortunately, nothing has changed ever since. SDL never published a new version where this problem is fixed; we are all waiting as well. It's a Windows problem which does not happen to a lot of people (never occurred on any of our and on most of our players' machines).
We also found out that some of the people who are experiencing the mouse click problem do not understand the controls of the game yet, because you can only open the menu for the interactions by holding the left mouse click a little longer, not by making a simple click.
The cut you hear is caused by bad editing of the sound files. It’s too sharp. With the update to the new engine version, the audio file format changed, which caused the problem to be more prominent, as the files were merged together some more and cut each other off. Unfortunately, this isn’t something we can fix for this game. But we'll try to avoid this in our current and future games and leave more room for the transitions.