Not sure if this is helpful for Mac users, but I found this issue and played with the options settings to fix it. Hope this is helpful.
[When using "Find & Replace", characters where getting substituted]
On Windows 10, using Control + H, I'd paste $(date "+%Y-%m-%d_%H-%M-%S") into the search field and it would substitute a double quote character " with " ;
My fix was to go into options (Tools --> Options --> Note) and Uncheck "Automatically format text elements"