Mouse settings can be locked in : Menu bar, Apple Menu, System Preferences, Mouse, "Click & Tap" tab
There will be a secion labeled "Clicks." Typicaly "One Finger Middle axis Click" will be checked, and set to "Middle Click." That means it you tap the mouse, down the vertical center of the magic mouse, it will trigure middle click instead of left click.
Try unchecking "One Finder Middle Axis click," and then see if you still have the issue.
I do not have those options. I go to Mouse settings pane, I see two tabs: Point & Click, and More Gestures.
In Point and Click, I have all three checkboxes checked: Scroll Direction, Secondary Click, Smart Zoom.
In More Gestures, all three checkboxes are UNchecked: Swipe between pages, Swipe between full screen apps, Mission Control.