yes, when you tighten a bolt, you get both plastic and elastic deformation.
Elastic deformation is stretching that goes back when the load is released. (Like a spring, it goes back when unloaded).
Plastic deformation is when the bolt stretches PERMANENTLY and does not go back when unloaded.
You cannot measure plastic deformation with the bolt under clamp load.
It is difficult to get an accurate reading for bolt length unless the bolts are ground flat/parallel and with centers drilled in them. Otherwise the ridges that are made when they form the bolt can throw off the measurements.
Try to measure a bolt 10 times and see if you get the same exact reading every time. If you can't, then your measurement method is not good enough....
You have to use micrometers, not calipers. Calipers are not sensitive enough...