-any substrate which will be associated with permanent outgassing will lead to an at least temporary contamination. Plastics with flexibilizing agents would come to mind as an example: if you try to put one of these in UHV, you will observe that you don't come below 10-5 mbar. This particular effect is reversible and after removing the outgassing substance your chamber may recover on its own.
-If you degas your sample thermally, there are of course many substances which can outgas upon heating. So be sure you know what temperature your material can withstand before turning up the heater. I know of a guy who used a plastic holder in an annealing experiment, in that case the chamber was permanently done for.
-X-Rays can also cause radiation chemistry and if you have that, volatile products may be generated. This last group is of course the hardest to predict since people often don't discuss it in papers, they just stop using the method when they realize it's happening.
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