Rough idle after engine swap?

Sha170

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Hi I have a Audi A3 1.6 TDI. It recently had a used engine put in that had only done 34k miles.
I've done approx 3k miles with it it's been perfect since the start however I noticed recently it's started developing a slightly rough idle. It shakes a little bit at first I thought I was imagining things however it has got a little bit more rough.

When the engine was swapped I did ask the mechanic if the injectors would need coding and he said no they would be fine, could this be the possible cause
 

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