I have just completed the Nikfgaard Connection after taking the 2nd peaceful option of scaring the guards off but I am instantly attacked when entering Crow's Perch and not allowed into the Castle. Is this a glitch or has something been changed with the update - or both? Is there a way to fix this?

You can find another way to reach the baron: the guards will not let you inside the castle proper, so you might find somebody (still inside the first walls) that will share some information about a secret entrance.

I used the 2nd option of telling them that I'm a witcher which is a peaceful option, but they attacked me on sight at Crows Perch as I entered the town. I did not get a option to bribe them.

Now wherever I go the peasants all shout to run and hide, even whilst casually milling around. I also cannot talk with the Blacksmith in Blackbough.

Did you meet any Bloody Baron cronies when you left the Inn? If you did, did a scuffle occur, or did you high-tail out of there? If the former, that's why they are hostile. If you didn't encounter further thugs outside the inn, did you go straight to Heatherton and then Crow's Perch? If you did, and you have a saved game before Inn at the Crossroads, I would suggest you start again from there, since you won't have lost much time -- Heatherton's a very short distraction.

I'll give it a try. Thanks for the reply.

Did quest again - no problems - made 2nd choice and did not need to bribe the guards. No idea who i aggro'd. Thanks again.

Cool. Glad you got it sorted.