Punctures carrying over from shakedown - Is this intentional?

I think that's intentional as all the damage you collect in shakedown runs will be carried over to the first stage unless you repair the car and/or change tires. So it seems to be the correct behaviour imo.

After shakedown you can change to a new set off tyres before you go to a stage.  Problem is you’ll have one less set for the event so you’ll have to workout if doing a 5 stage event.  How long the stages are and then decide which stage you decide to change the first set.  Which would be either after 2 and use next set for remaining 3 stages,  or visa versa.   On all stages except snow you’ll get a  softer option and a harder.  So obviously select the harder for 3 stage 

Yeah I also wondered about that.

I know that you can change it but I think in other stages if you have a puncture and start the stage after service your tires are automatically replaced (not 100% sure). I just know I was also surprised. Although I do see it as a positive that I have to pay attention

I have repaired the car, started the stage and the puncture was still there. I had to crash the game, loading me back, right after repairs, but before the stage start. I then had to change tyres, but that meant I had 1 set fewer for the rest of the rally. Normally that wouldn't ne a problem, but it was Months Carlo with winter tyres.