iTerm2 has a feature called "Hotkey window" which is a special Terminal window that slides in from the top of the screen upon pressing a special hotkey.

When I press the Terminal button in SourceTree, a new tab is created in this special window, although it is hidden, and an audible bell is played.

Expected behaviour would be to open a new "normal" iTerm2 window, although I don't know wether thats even possible from your side or a iTerm2 bug.
If you have no control over this, just close this bug