The hydrogen in the Space Shuttle Main Engine creates embrittlement in the alloys of the engine. [1][2] The launch sequence also involved running the engines at 104.5% of rated capacity. [3] Before Block II of the engines, the turbopumps needed to be disassembled and rebuilt between flights. [4]

I have no real idea how significant coking of the Merlin engine is, but the SSMEs were hardly "clean".

[1] https://en.wikipedia.org/wiki/Hydrogen_embrittlement [2] http://www.tms.org/Superalloys/10.7449/1991/Superalloys_1991... [3] http://www.interspacenews.com/FeatureArticle/tabid/130/Defau... [4] http://www.nasa.gov/sites/default/files/174534main_ssme.pdf