I’ve noticed this bug for a long time, even before Yosemite.
If I drag n’drop files from one tab to another, from then on TotalFinder steals the focus when I switch to other apps. It will remain in front until I click on the tab where the files where dragged from.
It happens every time I drag n’drop from tab to tab.
I made a screen capture to demonstrate the issue:
NB: it may be related to Totalfinder show up when drop & drag but I’m not sure so I’m still posting this separate issue.