Microchipping should not cause any issue - however several pups have reacted in a similar way to the second vaccination - yelping when touched and a little more "off colour" than usual (some even off the food for a while). There are several posts on here about this and it does tend to sort itself out after 24 / 48 hours or so.
I take it that you have had the second jab of Nobivac - at 10 weeks ? As we have heard more pups with this 10 week jab experience this period of being "off colour" than those with the 12 week Eurican second jab (again not a given but noted purely from experience of reading abut it) - But either way it does tend to right itself quite quickly. The most important thing is to ensure there is enough fresh water close to hand - keeping any dog hydrated is a very important thing.