Could short hairs that didn't fall out after procedure be blocking new hair growth? Should these hairs be taken out?

In general, the transplanted hairs will shed weeks after the surgery.  If you still have the transplanted hairs after 5 months (the stubbles that never went away), try washing your hair more thoroughly.  Different doctors have different opinions on if you should pull them out.  Thus, follow up with your doctor and ask what you should do. 

Usually the hair shaft falls off with the scabs.  The new hair will start to come in after three months and may take up to 18 months for all the hair to grow in.  However this average not the standard.  There are cases where the hair continues to grow out and does not fall off and that is normal.  Do not use tweezers to pull any hair out, just let them go through their own natural growth process. 

These hairs will sooner or later shed. They are never a problem for new hairs that start to grow. Usually, there is a lag time between the time the hairs shed (2-8 weeks) and the time the new hair grows (3-8 months). IF for any reason, there is an overlap between the two, pay no attention to it for when the new hair grows, the old hairs from the grafts that may persist beyond 8 weeks, will eventually shed