Using clean and demagnetized gage blocks is paramount. A gage block that has grease and grime on it will be inaccurate. You must also demagnetize all blocks that retain a magnetic field. Good electronic demagnetizers and gauss gages are common catalog items today. Eliminate nicks and burrs.
Gage blocks require good overall geometry to measure accurately.
Nicked, burred, or scratched measuring faces will not wring together well and will most likely provide anomalous readings. This procedure, if performed correctly, will not hinder the quality or integrity of the gage blocks. Note that different block materials will require other types of deburring stones. Varying environmental temperatures affect material size, especially when using two different materials in your application. If the temperature is fluctuating as well, the problem is compounded.