Doctor, why does the gutta-percha not reach all the way to the apex after we instrument with f1?

First, a file and gutta-percha reaching the same length does not mean that everything is problem-free. Many parameters must match for the file and gutta-percha to reach the same length.
If the file and gutta-percha do not reach the same length, the reasons include:
-Diameter standardization of gutta-percha cones
-Taper standardization of gutta-percha cones
-Whether the gutta-percha cones are produced by hand rolling or injection molding
-Diameter standardization of files
-Whether the gutta-percha cones and files have similar hardness
-Diameter and taper standardization of files
-File cross-section, cutting efficiency, number of uses and heat-treatment protocol
-The speed setting used with the file
-How many times the file has been taken to the apex and whether circumferential filing has been performed
-Whether there is anatomy in the canal that could cause the gutta-percha cones to catch
In short, getting this many parameters to match is a utopia, and a complete match between the file and gutta-percha can never be achieved.