Like the title says. Maybe some journal from a famous general that was ruined by a technique that was later found to damage old paper like lemon juice. Or maybe a piece of art that was exposed to too much humidity. Art restoration and history preservation had to go through some trial and error before we got it right. Any notable examples?
I think the award for poorest restoration effort unequivocally goes to Elias Garcia Martinez Cecilia Giménez for her unauthorised attempt at restoring a 100 year old Fesco in Sanctuary of Mercy Church near Zaragoza. She meant well, but there's a reason it takes many years of experience and training to become a professional art restorer.
Edit: Just realised Elias Garcia Martinez was the original artist, Cecilia Giménez was the 'restorer'.
This might not be quite the answer you're looking for, but not that long ago they permanently damaged King Tut's mask. The beard was accidentally snapped off, and they used epoxy to glue it back on (instead of properly restoring it).
There's been a recent snafu about a mosaic in Turkey that was apparently poorly restored. The restorer says the picture on the right isn't the final product, but has failed to provide a better picture proving their claims.
I believe that the Parthenon Marbles on display at the British Museum originally had some remnants of colour on them and they where "cleaned up" be the Museum officials.
I know that when the Dead Sea Scrolls were first being analyzed, that scholars would smoke in the room with the fragments, touch them with bare hands, and use regular tape to piece them together. There has been irreparable damage done to the ancient texts going so far as to ruin certain pieces.
[chronology of condition] (http://www.deadseascrolls.org.il/learn-about-the-scrolls/conservation?locale=en_US)
[further reading] (http://www.chabad.org/library/article_cdo/aid/1725431/jewish/What-Are-the-Dead-Sea-Scrolls.htm)