Apple - "Ghost text" in terminal, Yosemite + TotalTerminal (formerly Visor)
This one helped me:
Open your Terminal preferences, go to Profiles > Window > Background (Color & Effects), and set a light blur.
I use 30% to keep anything in the background from disturbing the readability of thin fonts on an already translucent window, so I never noticed the "burn-in" effect when moving to Yosemite.
Source: http://discuss.binaryage.com/t/text-burn-in-when-using-transparent-backgrounds-since-yosemite/2849
However I set blur to 1% and "ghost" text disappeared.
More recently in the thread linked to above, the developer of TotalTerminal replied:
darwin - Sep '15
TotalTerminal is not going to work on El Capitan without System Integrity Protection disabled. That is why I stopped developing it and switched personally > to iTerm2. I'm sorry, but I won't fix this one.
http://discuss.binaryage.com/t/text-burn-in-when-using-transparent-backgrounds-since-yosemite/2849/11
So it looks like we're out of luck, at least for now. I've noticed the ghosting for a while, and right now I'm actually running TotalTerminal on El Capitan (with SIP disabled I guess), and would love to keep using it, but it sounds like I'll have to take it with this little wart or not at all.