Transmission v1.72 (8709)
Safari 4.0.2 (5530.19)
Leopard 10.5.7
With Transmission's window open and behind Safari (which is in the foreground) if there is an overlap and the cursor is near the Total Ratio/Total Transfer info bar (the one you click on two see Total Ratio/Total Transfers) but atop Safari, the info bar in Transmission will highlight and react (un-highlight) when you click. You have to be below the bookmarks bar and above tabs. It's right about where a tab's top line is below things in the bookmarks bar.
It doesn't cause any problems but it's odd that an app beneath Safari will react to a cursor. It's almost as if there's a hole in Safari allowing the cursor to affect Transmission when it's behind Safari.
Small Interface Bug
Re: Small Interface Bug
Please try the latest Nightly Build and see if the issue is still there, as I'm writing this the latest is r8843 (you're using r8709).