Magic Mouse Left-Click Intermittently Doesn't Work Sometimes in Chrome
As it turns out, the problem only happens while Magnet is running:

https://productforums.google.com/forum/#!topic/chrome/03EmKuDuw5c;context-place=topicsearchin/chrome/category$3AStable%7Csort:relevance%7Cspell:false

I have contacted Magnet and asked fi they will release a fix to solve this problem. If they do, I'll post an update here.